Method and apparatus for radiation encoding an analysis

ABSTRACT

Method and apparatus for analyzing radiation using analyzers and encoders employing the spatial modulation of radiation dispersed by wavelength or imaged along a line.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a division of U.S. application Ser. No. 10/384,374,filed Mar. 6, 2003 now U.S. Pat. No. 6,995,840, which is incorporated byreference in its entirety, and which claims the benefit of U.S.Provisional Application No. 60/361,967, filed Mar. 6, 2002, and U.S.Provisional Application No. 60/413,424, filed Sep. 25, 2002.

BACKGROUND OF THE INVENTION

This invention relates in general to radiation spectrum analyzers andradiation image analyzers, and in particular, to radiation analyzers andencoders employing the spatial modulation of radiation dispersed bywavelength or imaged along a line.

Radiation spectral analysis is presently carried out in a number ofways. Dispersive and Fourier transform based analyzers are for highresolution and can be used for many different applications so that theyare more versatile than existing application-specific instruments andprocedures. While these analyzers offer superior spectral performance,they tend to be expensive, large, heavy and non-portable. For mostapplications, these instruments offer a spectral resolution that islargely unnecessary. Many analytical computations can be made usingrelatively few spectral measurements. The processing of the additional,unnecessary optical data reduces the speed and compromises thephotometric accuracy of these instruments.

In contrast, a non-dispersive approach to spectral analysis employs aradiation source filtered by one or more bandpass to provide input to aspecific analytical function. The bandpass filters are used to selectone or more specific spectral components, which are characterized by acenter wavelength and bandwidth. One of the principal advantages of thenon-dispersive approach is the ability to individually specify thecenter wavelength and bandwidth of the bandpass filters to optimize theinstrument for a particular application. However, if the analyticalfunction requires a significant number of bandpass filters, the system'ssignal-to-noise ratio is reduced as the total energy measured in a givenfilter over time is inversely related to the number of filters.Furthermore, if a spectrum analyzer using this approach is configuredfor a first application, the filters used in the device may have to bereplaced, or the number of filters changed, in order to adapt theanalyzer to a second application. As a consequence, the non-dispersiveapproach has clear limitation in adaptability and the number of spectralcomponents that can be analyzed.

Another type of optical spectrum analyzer, which is best described as ahybrid between dispersive and non-dispersive instruments, is theHadamard spectrometer. The Hadamard spectrometer includes a spatialradiation modulator, comprising a disc made of an opaque material withslots therein that reflect or transmit radiation, where the slots haveuniform transmittance or reflectance. A radiation beam is dispersedaccording to wavelength onto the disc and the slots are selectivelyspaced at different radii from the axis to form a number of differentoptical channels for detecting corresponding spectral components of thebeam. The disc is rotated about the axis and the slots selectivelyencode the corresponding spectral components with a binary amplitudemodulation. The encoded beam is then directed to a detector. In order todifferentiate the intensity of the spectral component transmitted orreflected by one slot from that of another, the disc is sequentiallystepped through a specific number of steps, each step comprising abinary pattern of open or closed optical channels, which defines oneequation in a system of simultaneous equations for the amplitudes of thespectral components. This set of simultaneous equations is then solvedto yield the intensity for each channel prior to any specific analyticalfunction, an approach which is time consuming and prone to errors. Forexample, as a direct consequence of the binary encoding approach, thereis no mechanism by which one can recover the actual signal levels if anyone of the signal levels changes substantially over the period ofrotation. It should be noted that the system of equation can besimplified if the slots are patterned such that the radiation istransmitted or blocked one spectral component at a time (e.g., afilter-wheel photometer). However, this approach changes the opticalduty cycle of each of the spectral components from its optimum value of50%, thereby degrading the signal to noise ratio. Finally, if a Hadamardanalyzer is configured for a first application, and the number of slotsis changed to adapt the analyzer to a second application, the dataacquisition and decoding algorithms must be changed as well, whichsignificantly limits the instrument's adaptability.

Radiation imaging is primarily carried out using detector arrays andCharge Couple Devices (CCDs). Much of the data analysis employed bythese techniques involves the mapping of the image onto a regular arrayof detector elements. A significant reduction in data analysis would berealized if the detector array elements could be configured for thespecific image measured in the application. Infrared detector arrays aresusceptible to background radiation, inter-detector-element drift and1/f noise. Imaging systems based on infrared detector arrays typicallyneed a large Thermo-Electric (TE) cooler and are very expensive. Becauseof their modest sensitivity, CCD-based imaging systems typically need aTE cooler and long exposure times in low light level application such asfluorescence imaging. A significant performance advantage could berealized in fluorescence imaging if the pixels of the CCD camera couldbe replaced with individual, inter-calibrated Photo-Multiplier Tubes(PMTs). Unfortunately, a low-cost, high-density detector array based ona PMT simply does not exist.

None of the above approaches is entirely satisfactory. It is, therefore,desirable to provide improved spectrum and image analyzers where theabove-noted disadvantages are avoided or significantly diminished, andwhere the encoding, data acquisition and decoding are both generalizedand significantly simplified such that the details of the spectrum orimage analyzer can be rendered to a single application specific hardwarecomponent.

SUMMARY OF THE INVENTION

This invention provides many advantages over the radiation analyzersdescribed above. In some embodiments, the intensity of the incidentradiation is modulated independent of the bandwidth and that theamplitude of the modulated signal is a smooth function or changesbetween three or more distinct levels of contrast as the modulator isrotated about an axis or otherwise reciprocated. One can implement amulti-channel orthogonal encoding scheme for arbitrary centerwavelengths and bandwidths and arbitrary radial intensity distributions.In this manner, the center wavelengths and bandwidths of the encodedchannels can be independently optimized for a specific application. Thebefore mentioned optical encoding scheme is combined with imaging opticsso that radiation from an extended source or collection of discretesamples can be imaged using a single detector. This allows one tocontrol the modulation depth on a channel-by-channel basis independentof the bandwidth, a design strategy which may be useful for balancingsignal levels in systems where one or more channels have adisproportionately large fraction of the total incident radiation. Thisallows one to group modulation channels into complementary pairs wherethe amplitude and phase of the resulting encoded component aredetermined by the relative portion of radiation incident on the twofilters comprising the pair. In this manner, intensity differences,wavelength derivatives, and the radial position of the center of anintensity distribution can be measured directly. This allows one to useone or more complementary filter pairs in conjunction with an expectedradiation component for calibration and alignment purposes. One may alsouse a dedicated light source and detector and a series of marks on themodulator to detect spindle wobble, vibrations or a misaligned modulatorpattern on the modulator substrate for calibration and alignmentpurposes. One can also measure a plurality of response radiationcomponents as a function of two or more excitation componentssubstantially simultaneously, enabling a fast, compact fluorescence,Raman or photo-refractive excitation/response analyzer. It is possibleto use modulation functions which are based on incomplete periods of therotation of the modulator, which can be used to eliminate varioushardware items, free up micro-processor resources, synchronize themovements of external mechanical devices, measure both the radialposition and the intensity of an imaged radiation component, andincrease the spatial or spectral resolution of the analyzer. Finally,one may measure a plurality of spectral components individually selectedfrom a collection of radiation emitting samples substantiallysimultaneously using a one-dimensional hyper-spectral imaging optic anda single channel detector.

In one embodiment of the invention, a spectrum analyzer comprising atleast one source providing radiation having at least one selectedspectral component, the spectral component having an intensity, a centerwavelength and a bandwidth. A first optic is used to collect, disperseand focus the radiation to form an image dispersed by wavelength alongan encoding axis onto an encoding plane. A two-dimensional spatialradiation modulator is rotated about a rotation axis and positioned inthe encoding plane so that the encoding axis is substantially along aradial axis of the modulator. The modulator has at least one radiationfilter at a radius from the rotation axis having a radial widthsubstantially defining the bandwidth of a corresponding spectralcomponent of the radiation. The filter modulates the intensity of thecorresponding spectral component substantially independent of thebandwidth to provide an encoded beam comprising at least one encodedcomponent, wherein the amplitude of the encoded component is a smoothfunction or changes between three or more substantially distinct levelsof contrast as the modulator is rotated about the rotation axis.Preferably, at least two of the filters have substantially orthogonalmodulation functions along an azimuthal axis. Most preferably, at leastone of the filters modulates the intensity of a spectral componentsubstantially according to a digitized replica (e.g., a halftonerepresentation) of a function of the form sin²(mθ+pπ/4), where θ is therotation angle of the modulator about the axis and m is an integer. Asecond optic is used to collect and direct the encoded beam onto adetector, and a computer is used to analyze the signals generated by thedetector in response to the encoded beam. Preferably, the computer usesa decoding algorithm to compute the amplitude of at least one encodedcomponent from the signals generated by the detector in response to theencoded beam. If radiation in two or more spectral ranges is to beanalyzed simultaneously, a number of dichroic mirrors can be used tofocus two or more dispersed images onto the modulator and two or moredetectors can be used to detect the encoded radiation.

In another embodiment of the invention, an image analyzer for analyzingthe radiation from an extended source having at least two spatialcomponents that emit, transmit or reflect radiation, comprises a firstoptic collecting and focusing radiation from the extended source to format least two corresponding images along an encoding axis onto anencoding plane. One example of an extended source is a collection ofdifferent samples which emit, scatter, transmit or reflect radiation. Inthis case the individual samples are imaged along an encoding axis ontoan encoding plane, such that each sample is focused at a substantiallydifferent point along the encoding axis. Another example of an extendedsource is one or more radiation sources which is filtered by two or morebandpass filters. In this case the radiation transmitted through (or,alternatively, reflected from) the collection of bandpass filters isimaged along an encoding axis onto an encoding plane, such that theradiation filtered by each bandpass filter is focused at a substantiallydifferent point along the encoding axis. Another example of an extendedsource is a radiation source combined with an optical system (e.g.,comprising one or more diffractive, beam splitting, or lens arrayelements—or various combinations thereof) to produce a plurality ofsubstantially identical sub-images substantially separated from oneanother along one or more spatial axes. A two-dimensional spatialradiation modulator is rotated about a rotation axis and positioned inthe encoding plane so that the encoding axis is along a radial axis. Themodulator has at least one radiation filter at a radius from therotation axis for modulating the intensity of a corresponding spatialcomponent to provide an encoded beam comprising at least one encodedcomponent. Preferably, the amplitude of the encoded component is asmooth function or changes between three or more substantially distinctlevels of contrast as the modulator is rotated about the rotation axis.Most preferably, at least one of the filters modulates the intensity ofa spectral component substantially according to a digitized replica(e.g., a halftone representation) of a function of the formsin²(mθ+pπ/4), where θ is the rotation angle of the modulator about theaxis and m is an integer. A second optic is used to collect and directthe encoded beam onto a detector, and a computer is used to analyze thesignals generated by the detector in response to the encoded beam.Preferably, the computer uses a decoding algorithm to compute theamplitude of at least one encoded component from the signals generatedby the detector in response to the encoded beam. If radiation from twoor more extended sources of radiation are to be analyzed simultaneously,the images from the extended sources can be focused onto differentsurfaces or different radial axes of the modulator and one or moredetectors can be used to detect the radiation. In the preferredembodiment of the image analyzer, the extended source will contain anumber of reference spatial components and the modulator will contain anumber of dedicated filters to provide feedback for the alignment of theimage onto the modulator pattern. For some applications, it may bedesirable to further analyze the spatially encoded radiation from theextend source for one or more spectral properties. This may be performedby inserting a spectrum analyzer or other wavelength filtering devicebetween the modulator and the detector.

In the preferred embodiment of the spectrum and imaging analyzersdescribed above, the two-dimensional spatial radiation modulatorcontains a series of timing marks and the analyzer has a number ofoptical switches which are triggered by the timing marks to establishthe absolute angle of rotation for decoding purposes. Most preferably,the timing marks will also trigger the data acquisition (DAQ) from thedetector and the decoding algorithm, which in turn, will substantiallyrelax any stability requirements of the modulators rotational period.Preferably, the analyzer will have a dedicated radiation source and ananalog detector which is partially interrupted by the timing marksand/or other marks located on the modulator or spindle to detect spindlewobble or a misaligned pattern on the modulator. More preferably, thesignal generated by the analog detector are processed by the computer toprovide the decoding algorithm and/or the analytical function with oneor more calibration coefficients used to compensate for the undesiredeffects of spindle wobble or a misaligned pattern. Most preferably, thesignal generated by the analog detector are processed by the computer toprovide a control signal to position of one or more optical elements tokeep the image or dispersed image centered on the modulator pattern.

In the preferred embodiment of the spectrum and imaging analyzersdescribed above, the analyzers computer will include a transient-signalalgorithm that will detect transients in the amplitudes of the encodedcomponents which occur during a rotational period of the modulator.Preferably, the computer will analyze the transient signal to determineits harmonic content. More preferably, the harmonic content will be usedby the decoding algorithm to compensate for transient-induced harmonicinterference. Preferably, the transient-signal algorithm will include afeedback mechanism to increase the motor speed in response to thedetection of sub-rotational-period signal transients and decrease themotor speed in response to extended periods of time where the amplitudesare stable.

Another aspect of the invention and useful for the above-describedspectrum and image analyzers is a spatial radiation modulator adapted tobe rotated about a rotation axis to modulate at least one component ofan incident radiation beam to provide an encoded beam. The modulatorcomprises a substrate and at least one radiation filter located at aradius from the rotation axis. The filter comprises an annular regionsubstantially encompassing a plurality of pixels having opticalcharacteristics substantially different from the substrate. The pixelsare patterned substantially within the annular region to modulate theintensity of a corresponding radiation component predominantly along anazimuthal axis to provide an encoded component such that the amplitudeof the encoded component changes between three or more substantiallydistinct levels of contrast as the substrate is rotated about therotation axis. Preferably, the density of the pixels is used to controlthe modulation depth of the encoded component. In this manner, theamplitudes of two or more encoded components can be balanced when one ofthe components has a disproportionate fraction of the total incidentradiation.

Another aspect of the invention and useful for the above-describedspectrum and image analyzers is a two-dimensional radiation modulatoradapted to be rotated about a rotation axis to modulate at least onecomponent of an incident radiation beam to provide an encoded beam. Themodulator is comprised a substrate and at least one radiation filterlocated at a radius from the rotation axis. The filter has substantiallycontinuously variable optical characteristics along an azimuthal axis,and the optical characteristics are continuously varied to modulate theintensity of a corresponding radiation component as a substantiallysmooth function of a rotation angle of the modulator about the rotationaxis.

Another aspect of the invention and useful for the above-describedspectrum and image analyzers is a two dimensional spatial radiationmodulator adapted to be rotated about a rotation axis, or otherwisereciprocated in a direction. The modulator includes at least oneradiation filter pair for modulating the intensity of an incidentradiation beam to provide an encoded beam comprising at least oneencoded component. The pair comprises two radiation filters located atdifferent radii from the rotation axis and having modulation functionsthat are complementary to each other so that the amplitude and phase ofthe resulting encoded component is determined by the relative proportionof radiation incident on the two filters. In that manner, the differencein the radiation intensity incident on the two filters can be measureddirectly rather than inferring the difference by subtraction, aninefficient approach which is prone to errors and which wastes thedynamic range of the detector signal. Preferably, the modulationfunctions are smooth functions or digitized replicas of smooth functionshaving three or more distinct levels of contrast. More preferably, themodulation functions of two filter pairs for modulating two differentradiation component differences are substantially orthogonal to oneanother.

Another aspect of the invention and useful for the above-describedspectrum and image analyzers is a two dimensional spatial radiationmodulator adapted to be rotated about a rotation axis, or otherwisereciprocated in a direction. The modulator includes at least oneradiation filter pair for measuring the difference in the radiationintensity incident on the two filters comprising the pair and a thirdradiation filter for measuring the sum of the radiation intensityincident on the two filters. In this manner, both the radial position ofthe center of the intensity distribution and the total intensity can bemeasured substantially simultaneously.

In some applications, it may be desirable to measure a samples responseto two or more different excitation components substantiallysimultaneously. For example, some samples are altered by the excitationradiation such that the results of the measurements may differ dependingupon which excitation component is first used in a series ofmeasurements employing different excitation components. Another examplewhere it may be desirable to measure a samples response to two or moredifferent excitation components substantially simultaneously is a samplewhich is flowing in a process stream where the dwell time of the sampleat the location of the measurement is insufficient to make theexcitation measurements in sequence. In another embodiment of theinvention, one or more excitation sources provide excitation radiationcomprising two or more distinct excitation components. For example, adiffractive or refractive optic may be used to spatially separate thespectral lines of a multi-line laser. The excitation components (e.g.,the spectral lines) are directed to the sample substantially insequence. In response to excitation radiation, the sample emits aresponse beam of radiation comprising at least one response componentemitted, transmitted, reflected or scattered in response to theexcitation radiation. The response beam of radiation is collected and animage or a dispersed image is formed along an encoding axis in anencoding plane. A two-dimensional spatial radiation modulator rotatedabout a rotation axis and positioned in the encoding plane so that theencoding axis is along a radial axis. The modulator has at least oneradiation filter at a radius from the rotation axis. The radiationfilter modulates the intensity of a corresponding response component toprovide an encoded response beam comprising at least one encodedresponse component. Preferably, the modulation functions of themodulator that encode the response components are smooth functions orare digitized replicas of smooth functions having three or more distinctlevels of contrast. The encoded response beam is collected and directedto a detector and the resulting signal is analyzed by a computer tocomputes the amplitude of at least one encoded response component as afunction of the two or more excitation components. Preferably, themodulator used to encoded the response components is also used fordirecting the components of excitation radiation to the samplesubstantially in sequence. Preferably, the excitation sequence issynchronized with the data acquisition of the encoded response beam sothat the response components corresponding to one excitation componentmay be distinguished from those corresponding to other excitationcomponents. More preferably, the time-based detector signal is sortedinto sub-signals, where each sub-signal corresponds to the encodedresponse components corresponding to only one of the excitationcomponents.

In another embodiment of the invention, an analyzer for monitoringradiation from at least one radiation source comprises an input beamcomprising at least one radiation component corresponding to a distinctradiation source and having an intensity and a center wavelength. Theinput beam is collected and dispersed to form at least one image alongan encoding axis onto an encoding plane, where the image corresponds tothe component. A two-dimensional spatial radiation modulator rotatedabout a rotation axis and positioned in the encoding plane so that theencoding axis is substantially along a radial axis such that a change inthe center wavelength of the component will cause the correspondingimage to move substantially along the radial axis. The modulator has atleast one radiation filter pair for modulating the intensity of acorresponding component to provide an encoded beam comprising at leastone encoded component. The filter pair comprises two radiation filterslocated at different radii from the rotation axis and having modulationfunctions that are complementary or out of phase so that the amplitudeand phase of the encoded component is determined by the relativeproportion of radiation incident on the two filters. Preferably, theradiation filters comprising the pair are substantially adjacent to oneanother. More preferably, the border between the adjacent radiationfilters is substantially located at the radius which correspond to thenominal or desired center wavelength for the radiation source. Theencoded beam is collected and directed to a detector and a computeranalyzes the signals generated by the detector in response to theencoded beam. Preferably, the computer computes the amplitudes andphases of at least one encoded component from the signals generated bythe detector in response to the encoded beam. More preferably, thecomputer generates at least one control signal for adjusting the centerwavelength of at least one source in response to the signals generatedby the detector to tune the source. Preferably, at least two of theencoded components are encoded with substantially orthogonal modulationfunctions, and computer computes the amplitude and phase of at least oneof the encoded component. Preferably, each of the modulation functionsis a smooth function or a digitized replica of a smooth function havingthree or more distinct levels of contrast. Preferably, the analyzer willhave one or more optical elements on movable stages such that the imagescan be collectively displaced along the radial axis of the modulator. Inthis manner, the instrument can be calibrated, and periodically, thesource images can be purposely offset with respect to the filter pairson the modulator in order to measure the intensity of the radiationsources. More preferably, the modulator can be segregated into twohalves, the first half containing complementary pairs for monitoring thewavelength and the second half containing individual filters to measurethe intensity. In this manner, the analyzer can provide a control signalto stabilize the sources wavelength and measure the sources intensity.By adding addition filter pairs that are orthogonal to other filterpairs, more than one radiation source may be monitored at the same time.

In the embodiments below, radiation provided by a source is directed toform images along an image axis onto a plane. A two dimensional spatialradiation modulator is rotated about a rotation axis and positioned inthe plane so that the image axis is substantially along an encoding axisof the modulator, the modulator modulating the intensity of the spectralcomponents to provide an encoded beam comprising at least two encodedcomponent, where the encoding axis is substantially along a radial axis.The modulator has at least two radiation encoding filters at differentradii from the rotation axis for modulating intensities of radiationfrom the source as the modulator is rotated about the rotation axis.

In one embodiment, a radiation spectrum analyzer employs a bi-conicoptical element to reduce the optical path length between the modulatorand the detector, and/or to increase the collection efficiency. Thecurvature of the bi-conic optical element may be chosen so as toincrease the collection efficiency.

In another embodiment, radiation is dispersed by wavelength according toa dispersion function on the modulator. The modulator has filtersthereon with radial positions and radial widths that are functions ofthe spectral properties of certain analytes and the dispersion function.Radiation modulated by the filters can be analyzed to determine presenceof one or more of the analytes. The modulator can be designed byconstructing a chemometric matrix to relate concentrations of theanalytes to intensities of spectral components in the radiation,deriving from the chemometric matrix optimized spectral windows, andtranslating the optimized spectral windows into a correspondingoptimized annular region or annular segment on the modulator using thedispersion function.

In still another embodiment, filters on the modulator have substantiallycomplementary modulation functions so that each pair of complementaryradiation filters produces a single encoded calibration component whereat least one characteristic of the encoded calibration component isdetermined by the relative intensities of radiation from a beam incidenton the two filters, wherein the radial position and radial width of theannular regions are such that a predetermined value for the singleencoded calibration component is produced as the modulator is rotatedabout the rotation axis. The encoded calibration component(s) aredetected for gauging the displacement of position of a known spectralfeature in the dispersed image from an aligned position along theencoding axis.

In yet another embodiment, the modulator has at least two radiationfilters substantially occupying a common annular region at a radius froma rotation axis. The filters modulate the intensity of substantiallyequal portions of corresponding radiation components of a beam atdifferent modulating frequencies to provide an encoded beam comprisingat least two encoded calibration components as the modulator is rotatedabout the rotation axis, the encoded calibration components havingsubstantially different frequencies. The encoded calibration componentsare detected to determine frequency dependence of a detection system.

In still another embodiment, an encoded filter-correlation radiometerincludes at least two target wavelength filters, the target wavelengthfilters having substantial optical absorbance in the spectral range andat least one reference wavelength filters, each of the referencewavelength filters having substantially less optical absorbance in thespectral range as compared to the target analytes. Radiation separatelypassing through the filters are used to measure a sample, and detectedto measure characteristics of the sample.

In one more embodiment, an encoded filter-correlation radiometer formeasuring a sample comprises at least one target and referencewavelength filter pair, the target wavelength filter in the at least onepair having substantial optical absorbance in the spectral range and thereference wavelength filter in the at least one pair havingsubstantially less optical absorbance in the spectral range as comparedto the target analytes. Radiation transmitted separately through thetarget wavelength filter and the reference wavelength filter is incidenton a modulator of the type described as the modulator is rotated aboutthe rotation axis and is detected. Radiation that is so detected in anoptical path in which a sample is placed is useful for measuring asample.

In still one more embodiment, optics providing in response to an encodedbeam a substantially collimated encoded beam is used so that large ordistant objects and media can be measured.

In one more embodiment, radiation in different spectral ranges ismodulated by a modulator of the type described above and detectedseparately. Such scheme is useful for measuring samples.

Yet another embodiment is directed to a two dimensional spatialradiation modulator adapted to be rotated about a rotation axis tomodulate at least one component of an incident radiation beam to encodethe beam, the modulator comprising:

-   -   a substrate and at least one annular region substantially        encompassing a plurality of non-contiguous sub-regions having        optical characteristics substantially different from the        substrate, the annular region comprising at least two annular        segments, each the segment comprising a fractional rotation        period of the modulator,    -   the sub-regions in a first annular segment being patterned to        form at least one pair of radiation filters located at different        radii from the rotation axis and having substantially        complementary modulation functions, the pair producing in        response to the beam a first encoded component with a        characteristic determined by the relative intensities of        radiation from the beam incident on the at least one pair of        filters;    -   the sub-regions in a second annular segment being patterned to        form at least one radiation filter that produces in response to        the beam a second encoded component with a characteristic        determined by the total intensity of radiation from the beam        incident on the at least one radiation filter.

One more embodiment employs a modulator having at least one annularregion comprising at least two annular segments, each segment comprisinga fractional rotation period of the modulator, wherein the sub-regionswithin the segment of the at least one radiation filter are beingpatterned to modulate the intensity of a corresponding radiationcomponent in a beam with a periodic function directed to the modulatorto provide an encoded beam comprising at least one encoded component asthe modulator is rotated about the rotation axis, the periodic functioncomprising substantially a harmonic of the active sub-period. Themodulator has at least another one of the segments being substantiallyoptically passive when interacting with the beam during a passivesub-period of the rotation period.

In still one more embodiment, rotation frequency of a modulator of thetype described above is controlled. Signals generated by a detectordetecting modulated signals are analyzed, wherein the analyzing includesdecoding at least one noise tracking signal originating from a periodicnoise source. The rotation frequency of the modulator is varied tomaximize an amplitude of the noise tracking signal and thereby minimizethe effect of the periodic noise source on the decoded amplitudes ofcertain encoded components.

In yet another embodiment, a modulator has a complementary pair havingsubstantially complementary modulation functions so that an encoded beamobtained by directing a beam of radiation to the modulator comprises acomponent with a characteristic determined by the relative intensitiesof radiation from the beam incident on the two filters. The encoded beamis detected and the result analyzed to determine the characteristic as afunction of the rotation angle of the modulator about the rotation axisto gauge the concentricity of the annular segment or region with respectto the rotation axis.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A is a schematic side view of multi-purpose radiation analyzer 100to illustrate the preferred embodiment of the invention.

FIG. 1B is a schematic view illustrating a view along the line 1B-1B inFIG. 1A of a portion of the analyzer in FIG. 1A.

FIG. 1C is a schematic view illustrating an embodiment of analyzer 100that encodes and analyzes radiation in two distinct spectral ranges.

FIG. 2 is a top view of embodiment 22A of modulator 22, suitable for usein analyzer 100 of FIG. 1 to illustrate an embodiment of the invention.

FIG. 3A is a graphical plot of a digitized replica of a smoothmodulation function illustrating one embodiment one of the radiationfilters of FIG. 2.

FIG. 3B is a plot showing the effects of finite digitization on thenominally orthogonal amplitude wavefunctions.

FIG. 4A is an illustration of the focal plane of the spectrum analyzerembodiment of analyzer 100 of FIG. 1A. FIG. 4B is an illustration of thefocal plane of the image analyzer embodiment of analyzer 100 of FIG. 1A.

FIG. 5 is a top view of embodiment 22B of modulator 22, suitable for usein analyzer 100 of FIG. 1 to illustrate an embodiment of the invention.

FIG. 6 is a top view of embodiment 22C of modulator 22, suitable for usein analyzer 100 of FIG. 1 to illustrate an embodiment of the invention.

FIG. 7 is a top view of embodiment 22D of modulator 22, suitable for usein analyzer 100 of FIG. 1 to illustrate an embodiment of the invention.

FIG. 8 is a top view of embodiment 22E of modulator 22, suitable for usein analyzer 100 of FIG. 1 to illustrate an embodiment of the invention.

FIG. 9A is a schematic view of analyzer 100 that includes a foldingmirror whose position is moveable to illustrate a preferred embodimentof the invention.

FIG. 9B is a schematic side view of the Alignment Calibration andTracking Analyzer embodiment of analyzer 100.

FIG. 9C is a top view of embodiment 22F of modulator 22, for use in theAlignment Calibration and Tracking Analyzer embodiment of analyzer 100.

FIG. 10A is a schematic view of analyzer 300, useful for measuring theoptical characteristics of a sample when excited by means of twodistinct excitation sources.

FIG. 10B is a top view of embodiment 322 of modulator 22, for use inanalyzer 300 of FIG. 10A.

FIG. 11A is a top view of embodiment 22DZ of modulator 22, whichincorporates radiation filters which are based on harmonics of anincomplete rotational period.

FIG. 11B is a top view of embodiment 22G of modulator 22, illustratingtwo methods to increase the spatial resolution of the encoding of targetimage 52.

FIG. 12A is a first schematic side view of embodiment HS of pre-encoderoptic 36A of FIG. 1A.

FIG. 12B is a second schematic side view of embodiment HS of pre-encoderoptic 36A of FIG. 1A.

FIG. 12C is a top view of embodiment 22HS of modulator 22 to be used inthe Hyper-Spectral Imaging Analyzer embodiment of analyzer 100.

FIG. 13A is a schematic representation of one method to configurationmodulator 22 for the Multivariate Chemometric Analyzer embodiment ofanalyzer 100.

FIG. 13B shows embodiment 22HC of modulator 22, for use in theMultivariate Chemometric Analyzer embodiment of analyzer 100.

FIG. 13C shows the respective transmission spectra of five hydrocarbons,and the corresponding optimized spectral windows for use in theMultivariate Chemometric Analyzer embodiment of analyzer 100.

FIG. 14A illustrates the relation between the transmission spectra ofmethane and carbon dioxide and the optimized calibration spectralwindows, for use in the Spectral-Calibration Analyzer embodiment ofanalyzer 100.

FIG. 14B shows two normalized calibration curves obtained for thespectral absorbance features of CH₄ and CO₂ in the 3.0 to 4.5 micronregion, respectively, for use in the Spectral-Calibration Analyzerembodiment of analyzer 100.

FIG. 14C shows embodiment 22SC of modulator 22, for use in theSpectral-Calibration Analyzer embodiment of analyzer 100.

FIG. 14D illustrates the relation between the transmission spectra ofmethane and carbon dioxide and the optimized calibration spectralwindows T_(SC.1) through T_(SC.4), for use in the Spectral-CalibrationAnalyzer embodiment of analyzer 100.

FIG. 15 is a top view of embodiment 22FD of modulator 22 of FIG. 1A, tobe used with Detection-System Frequency-Dependence CompensationAnalyzer.

FIG. 16A is a schematic of the SP1 (Short-Path, Post-Encoder Optic)embodiment of post-encoder optic 36B of FIG. 1.

FIG. 16B is a graph of the encoded-component collection efficiency forthe SP1 (Short-Path, Post-Encoder Optic) embodiment of post-encoderoptic 36B of FIG. 1.

FIG. 16C is a schematic side-view of the SP1 (Short-Path) embodiment ofpost-encoder optic 36B of FIG. 1.

FIG. 16D is a schematic side-view of the SP2 (Short-Path) embodiment ofpost-encoder optic 36B of FIG. 1.

FIG. 17A is a schematic top-view of the Encoded Filter-PhotometerAnalyzer embodiment of radiation analyzer 100.

FIG. 17B is a schematic side-view of the Encoded Filter-PhotometerAnalyzer embodiment of radiation analyzer 100.

FIG. 18 is a schematic side-view of the Phase-Locked Noise-RejectionAnalyzer embodiment of radiation analyzer 100.

FIG. 19A is a schematic side-view of the Pattern Concentricity Analyzerembodiment of radiation analyzer 100.

FIG. 19B is a top view of one embodiment of modulator 22 to be used withPattern Concentricity Analyzer.

For easier reference, embodiments described below in the examples of aparticular element or system in the figures herein are typically givencomposite symbols, such as the number of the element in the figuresherein, followed by a decimal point and a number or followed by letters.For example, 100.1 is the number in an example below of one embodimentof the analyzer 100, where this embodiment is different from anotherembodiment 100.2 of the analyzer 100. 36A(HS) is an embodiment of thepre-encode optic 36A. Where an embodiment includes more than onecomponents, the composite symbol comprises the number of the element inFIG. 1A or other figures herein, followed by a decimal point, a firstnumber or letters indicating an embodiment of the element, and followedby another decimal point and a second number to indicate a particularcomponent of such embodiment. In example 1, for example, 36B.1.1 and36B.1.2 indicate the first and the second components respectively of thefirst embodiment of post-encoder optic 36B in FIG. 1A or other figuresherein. These composite symbols are not shown in FIG. 1A or otherfigures herein to simplify the figures. Additional components introducedby the examples will be given unique symbols.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENT

Because the present invention can be configured as a spectrum analyzer,as an image analyzer, or as a hyper-spectral image analyzer, it isconvenient to generalize certain terms and phrases used in thedescriptions that follow. In the descriptions of the present inventionthat follow we shall use the following multi-purpose notation forbrevity:

-   -   1. radiation source: radiation sources having spectral        components, radiation sources having spatial components, or        radiation sources having both spectral and spatial components.        The radiation source can be a sample or collection of samples        that emit, scatter, transmit or reflect radiation in response to        one or more components of excitation and/or probing radiation.    -   2. radiation components: portions of the radiation from the        radiation source having spectral information, portions of the        radiation from the radiation source having spatial information,        or portions of the radiation from the radiation source having        both spectral and spatial information.    -   3. pre-encoder optics: one or more optical elements which form        one or more images, or one or more dispersed images on a surface        of the modulator. The pre-encoder optic may include one or more        optical fibers, wave guides, or light pipes, for coupling        radiation from one or more remote sources to the analyzer. The        pre-encoder optic may include one or more open paths and one or        more remote reflectors. The pre-encoder optic may include        microscope or telescope optics.    -   4. post-encoder optics: one or more optical elements which        collect the encoded radiation from the modulator and direct and        focus the encoded beam onto one or more radiation detectors. The        post-encoder optic may include one or more optical fibers, wave        guides, or light pipes, for coupling encoded radiation from the        instrument to one or more remote sampling stations. The        post-encoder optic may include one or more open paths and one or        more remote reflectors. The post-encoder optic may include        microscope or telescope optics.    -   5. target image: an image comprising two or more radiation        components substantially separated from one another along an        encoding axis. The width of the target image is the spatial        extent perpendicular to the encoding axis.    -   6. imaging: collecting and focusing the source radiation to form        one or more images, one or more hyper-spectral images, or        collecting, dispersing and focusing the source radiation to form        one or more dispersed images along a common axis.    -   7. alignment components: anticipated or engineered radiation        components which are used in conjunction with dedicated filters        and/or complementary filter pairs to gauge the alignment of the        target image onto the modulator pattern.    -   8. detector: one or more radiation detectors and associated        electronics. The associated electronics may include bias        electronics, programmable gain, and one or more analog filter        networks (e.g., anti-aliasing filters).    -   9. sample: can be any solid, liquid or gas, such as one or more        gasses, liquids and/or solids that absorb, transmit, or scatter        (e.g., reflect, Raman scatter, Raleigh scatter) incident        radiation. Samples may emit one or more response components of        radiation in response to one or more components of excitation        radiation. Samples may be confined by a vessel or cell or may be        unbounded (e.g., the atmosphere).

Radiation Analyzer/Encoder 100

FIG. 1A is a schematic side-view of multi-purpose radiation analyzer 100(which can be configured as a spectrum analyzer, an image analyzer, ahyper-spectral imaging analyzer, or an encoded source of excitation orprobing radiation), to illustrate a preferred embodiment of theinvention where the encoding of the selected spectral or spatialcomponents is achieved by spatially varying the reflectance propertiesof a rotating spatial radiation modulator. As shown in FIG. 1A, analyzer100 includes a spatial radiation modulator 22, which comprises pattern21 formed on a surface of modulator substrate 23, for encoding radiationfrom a source 24, which may be a broadband or multiple wavelength sourcecontaining spectral information, an extended source containing spatialinformation, or any combination thereof. The input radiation beam 54from source 24 is preferable passed through an entrance aperture 32 to afolding mirror 34 which reflects the radiation to pre-encoder optic 36Awhich images the input radiation to form target image 52 onto modulator22 such that the radiation components of 52 are focused at substantiallydifferent points along a radial axis of modulator 22. If more than onetarget image is to be encoded substantially simultaneously, additionaloptical elements (not shown) can be used to focus two or more targetimages onto modulator 22 and collect and direct the encoded beams ontoone or more radiation detectors.

Modulator substrate 23 rotates on a motorized spindle 42 about arotation axis 40 in the encoding plane. Preferably, modulator 22contains a sub-pattern of timing and/or location marks that interruptthe optical switches described below for timing and alignment purposes.More preferably, this sub-pattern includes at least two series of marksconfined to annular regions at different radii, one series having marksat regular angular intervals and the other series having marks atnon-regular angular intervals. In this manner, the exact rotation angleof modulator can be established by computer 28 for decoding purposes.Modulator 22 has at least one radiation filter at a radius from rotationaxis 40 which modulates (or encodes) the intensity of a correspondingradiation component to provide an encoded beam comprising at least oneencoded component 56 (e.g., 56.1), wherein the amplitude of the encodedcomponent is a smooth function or changes between three or moresubstantially distinct levels of contrast as the modulator is rotatedabout rotation axis 40. For convenience in description, the spatialradiation filters on modulator 22 are described to reflect radiation, itbeing understood that spatial radiation filters that transmit instead ofreflect radiation may be used instead in each of the embodiments hereinand such variations are within the scope of the invention. The encodedradiation beam 56 (shown in FIG. 1 to be reflected by modulator 22) iscollected, directed and focused by post-encoder optic 36B towardsfolding mirror 34, which reflects encoded beam 56 towards an exitaperture 44 onto detector 26. Preferably, the encoded components (e.g.,56.1 and 56.2) substantially overlap one another on the surface ofdetector 26. Detector 26 detects the total intensity of the differentencoded radiation components in the encoded beam to provide detectoroutput 27 to computer 28.

As shown in FIG. 1A, in many embodiments of analyzer 100, sample 38 isinserted in the optical path between source 24 and detector 26. In anumber of embodiments, sample 38 is a sample cell filled with a samplegas or liquid. In some embodiments, sample cell 38 comprises one or moreabsorbing media 37, which collect analytes adsorbed over time. Absorbingmedia 37 can be augmented with heater 39, which heats absorbing media 37to desorb one or more adsorbed analytes. If the analytes desorbed fromabsorbing media 37 by heater 39 are confined by sample cell 38, theconcentration of analytes in sample cell 38 is enriched. Examples ofsample 38, absorbing media 37, and heater 39 are described below.

As an option, analyzer 100 includes remote detector RD26 and remotecomputer RD28 for use in applications described below. Remote detectorRD26 and remote computer RD28 are similar to detector 26 and computer28, respectively, but are located at one or more remote locations.

The optical geometry illustrated in FIG. 1A was chosen for clarity, asit has a small number of optical components. For example, as shown inFIG. 1A, pre-encoder optic 36A and post-encoder optic 36B are combinedinto a single optical element. Other optical geometries which involveseparate, and more elaborate optical systems to collect and focus theinput radiation onto modulator 22 and to collect and focus the encodedbeam from modulator 22 onto detector 26 may be used instead in each ofthe embodiments herein and such variations are within the scope of theinvention.

In embodiments of analyzer 100 that excite radiation emitting orradiation scattering samples, a second post-encoder optic (e.g., 36B isreplaced by 36B.1 and 36B.2, not shown in FIG. 1A) may be useful. Forexample 36B.1 is used to collect encoded excitation radiation and directthe encoded excitation beam onto one or more samples. In response to theexcitation radiation, the samples emit or scatter one or more componentsof response radiation, and 36B.2 is used to collect the encoded responseradiation from the excited sample(s) and direct the encoded responsebeam onto detector 26. Such and other variations are within the scope ofthe invention.

Preferably, additional optical elements (e.g., fold mirrors) thatsubstantially confine the optical components to one or more planesparallel to the plane of modulator 22 are useful for reducing the sizeof the instrument. More preferably, the optical elements of theinvention are substantially confined two planes substantially parallelto the plane of said modulator. In this manner, the assembly and theoptical alignment procedures are simplified. More preferably, in each ofthe two planes, the individual optical elements are combined into asingle monolithic optic (e.g., by injection molding) to further simplifythe alignment procedure and reduce cost.

In another embodiment of the present invention, detector 26 can bereplaced with an optical fiber bundle and a number of remote samplingstations which include detector RD26 and computer RC28. In this manner,a number of remote measurements can be made substantially simultaneouslyby propagating the encoded beam to the remote measurement sites usingthe optical fibers or other suitable means. Preferably, the timingsignals generated by the optical switches described below are dispatchedalong with the encoded beam such that the data acquired at the remotelocations can be properly analyzed.

FIG. 1B is a view of the entrance and exit apertures 32, 34 along thearrow 1B-1B in FIG. 1A. Also shown in FIG. 1A is an xyz axis, so thatthe view along the arrow 1B-1B is along the negative x axis. A sampleand/or optical fiber (not shown) may be placed between the source andthe entrance aperture or between the exit aperture 44 and the detector26 for analysis.

Computer 28 includes an analog to digital converter 28.adc, a sub-signalseparator algorithm 28.sss (described below), a decoding algorithm28.dec, an application specific analytical function 28.asf, and bothanalog and digital outputs, 28.dac and 28.dig, respectively. Preferably,the detectors analog output is sampled by Analog-to-Digital Converter(ADC) 28.adc which is triggered by a first optical switch, 70,comprising radiation source 78 a and photodetector 79 a. A secondoptical switch, 71, comprising radiation source 78 b and photodetector79 b, provides the computer with a reference of 0 degrees to synchronizethe output of 28.adc with the decoding algorithm. Preferably, the analogoutputs of computer are used to interface to existing analyticalinstrument interface protocols. More preferably, the digital output ofcomputer 28 includes a connection to the Internet, a local area networkor a wireless network so that a number of remote instruments can bemonitored from a central location. As will be described below, as taughtby this invention, the filters in or on modulator 22 are such that theoptimum 50% duty cycle is retained and computer 28 can determine theamplitude of each radiation component encoded by modulator 22, withouthaving to solve a simultaneous system of equations for arbitrary radialintensity distributions in target image 52.

Computer 28 also includes set of utility algorithms 28.utl, includingMotor Control Algorithm (MCA), Motorized Stage Control (MSC), TransientSignal Algorithm (TSA), Alignment Calibration Algorithm (ACA), AlignmentTracking Algorithm (ATA), Frequency Compensation Algorithm (FCA), NoiseSearch Algorithm (NSA), Noise Phase Locking Algorithm (NPL), and PatternConcentricity Analysis (PCA). These algorithms are described below.

An alignment probe, 72, shown in FIG. 1A, comprising radiation source 78c and photodetector 79 c, is positioned such that the alignment beamemitted by 78 c and collected by 79 c is partially interrupted by thetiming marks and/or additional location marks (not shown) on modulator22. Preferably, the alignment beam is positioned such that the marks atregular angular intervals obscure roughly half of the alignment beam andthe marks at non-regular angular intervals obscure roughly the otherhalf of the alignment beam. More preferably, the alignment beam issubstantially centered one or more complementary filter pairs (describedbelow), such that the magnitude and phase of the signal produced byphotodetector 79 c is directly related to the concentricity of modulatorpattern 21 with respect to axis of rotation 40. Most preferably, themagnitude and phase of photodetector 79 c are used as feedback in themanufacturing process to properly align modulator 22 onto motorizedspindle 42. The analog output of alignment probe 72 is analyzed byAlignment Tracking Algorithm to gauge the error in the absolute positionof the radiation filters with respect to the axis of rotation. Thispositional error can arise from the manufacturing process of themodulator (e.g., the modulator pattern is printed off center on thesubstrate, resulting in a periodic error), from the wobble of thespindle (resulting in a dynamic, periodic or non-periodic error), orfrom the thermal expansion of the substrate (resulting in a staticradial error). Preferably, the output of Alignment Tracking Algorithm isused as input to the application specific analytical function 28.asf tocompensate for the effects of the error in the absolute position of theradiation filters with respect to the axis of rotation. More preferably,the output of Alignment Tracking Algorithm is used in AlignmentCalibration and Tracking Analyzer (shown below in FIG. 9B), whichdynamically positions one or more optical elements to keep target image52 properly aligned on modulator 22 as substrate 23 rotates about axis40.

In some applications it is useful to analyze radiation in two or moredistinct spectral ranges. For example, in the analysis of chemicalcompositions, improved specificity (or discrimination) can be achievedby looking at a number of spectral features in two or more distinctspectral ranges. Examples of distinct spectral ranges include spectralranges where a first detector type (e.g., PbSe) is optimized forradiation detection in the first spectral range (e.g., 3 to 5 microns),and a second detector type (e.g., HgCdTe) is optimized for radiationdetection in a second spectral range (8 to 12 microns). Other examplesof distinct spectral ranges include spectral ranges which are subject tointerference to one or more interfering gasses and vapors (or liquids)which can unpredictably affect the accuracy of the spectralmeasurements. Ambient carbon dioxide (CO₂) is a well know case in point.

FIG. 1C is a schematic view of an embodiment of analyzer 100 thatencodes and analyzes radiation in two distinct spectral ranges.Radiation source 24.SR1 provides radiation in a first spectral range.Pre-encoder optic 36A.SR1 collects radiation 54.SR1 from source 24.SR1,and forms target image 52.SR1 on a first surface of modulator 22.Post-encoder optic 36B.SR1 collects and directs encoded beam 56.SR1 ontodetector 26.SR1, which provides signal 27.SR1 in response to 56.SR1.Detector signal 27.SR1 is sampled by 28.adc.1 and decoded by 28.dec.1.In a similar fashion, radiation source 24.SR2 provides radiation in asecond spectral range. Pre-encoder optic 36A.SR2 collects radiation54.SR2 from source 24.SR2, and forms target image 52.SR2 on a secondsurface of modulator 22. Post-encoder optic 36B.SR2 collects and directsencoded beam 56.SR2 onto detector 26.SR2, which provides signal 27.SR2in response to 56.SR2. Detector signal 27.SR2 is sampled by 28.adc.2 anddecoded by 28.dec.2. The decoded components from both 56.SR1 and 56.SR2are used as input to 28.utl and 28.asf.

As shown in FIG. 1C, sample 38.SR1 is probed with encoded radiation inthe first spectral range, and sample 38.SR2 is probed with radiation inthe second spectral range. In some instances, it may be useful to probethe same sample with radiation in both spectral ranges. Such and othervariations are within the scope of the invention.

FIG. 2 is a top view of a radiation modulator with four differentradiation intensity filters thereon to illustrate an embodiment of theinvention. As shown in FIG. 2, modulator 22A includes four radiationfilters 50 a, 50 b, 50 c and 50 d. These filters may be formed as apatterned layer of radiation reflective material on top of a nonreflective substrate, or as a patterned layer of non-reflective materialon top of a reflective substrate; alternatively, these filters may beformed as patterned radiation transmissive areas in an opaque substrateor as a patterned layer of opaque material on a transmissive substrate.For convenience in description, the radiation intensity filters aredescribed to reflect radiation, it being understood that radiationintensity filters that transmit instead of reflect radiation orintroduce a phase difference may be used instead in each of theembodiments herein and such variations are within the scope of theinvention. In modulator 22A, the four radiation filters 50 a, 50 b, 50 cand 50 d are centered at non-regular intervals along the radial axis andhave different radial widths. In the preferred embodiment, the radialposition, radial width and modulation depth of the radiation filters areindividually optimized for a particular analytical function 28.asf.Modulator 22A also includes a number of timing marks at regular angularintervals 60 and one or more timing marks at non-regular angularintervals 61.

Preferably, the timing marks are reflective and the sources 78 a, 78 band 78 c and the photodetectors 79 a, 79 b and 79 c are located on thesame side of the modulator. In this manner, sources 78 a, 78 b and 78 cand the photodetectors 79 a, 79 b and 79 c can be mounted on the same PCboard: Alternately, the substrate is transmissive to the timing beam andtiming marks obstruct the timing beam or the substrate is opaque to thetiming signal and timing marks are milled or etched through substrate.Therefore, the output of photodetector 79 b may supply through aconnection to computer 28 to mark the zero rotational angle mark 61, and79 a may supply through a connection to also mark the instances of thepassage of each of the timing marks 60. Such instances may be utilizedby computer 28 for the phase-sensitive sampling of the output fromdetector 26 as modulator 22 is rotated about rotation axis 40.

More preferably, timing marks 60 and 61 and optical switches 70 and 71are replaced with a commercially available Incremental Rotary Encoder(IRE) mounted co-axially with modulator 22 along rotation axis 40. Thesynchronization of the signals from the IRE to the rotation of modulator22 is described below.

Radiation Intensity Filters

In the preferred embodiment, the radiation filters of the presentinvention have modulation functions that are digitized approximations,or replicas (e.g., a halftone representation) of the functionssin²(mθ+pπ/4), wherein m is an integer. Filter 50 a, for example, is adigitized approximation of the modulation function sin²(3θ), filter 50 bthat of modulation function sin²(5θ), filter 50 c that of sin²(7θ) andfilter 50 d that of sin²(9θ). As shown in FIG. 2, the reflectance ortransmittance of each of the radiation filters 50 a-50 d varies as adistinct function of the rotational angle θ of modulator 22A around therotational axis 40. At any given rotational angle of modulator 22A withrespect to the target image 50, the amplitude of the modulated radiationis given by the fraction of radiation that is reflected by (ortransmitted through) the non-contiguous radiation filter. As modulator22A is rotated about axis 40 radiation component 52 a is focused ontodifferent portions of radiation filter 50 a. Thus, as the modulator 22Ais rotated, radiation component 52 a is encoded by the angle-dependentreflectance of radiation filter 50 a.

As shown in FIG. 2, active area 53 a comprises the overlap of targetimage 52 and the annular region encompassing radiation filter 50 a. Therelative intensity of encoded component 56 a (reflected or transmitted)is given by the ratio of the sum of the areas of the non-contiguousregions of 50 a within 53 a to the total area of 53 a (appropriatelyweighted by the intensity distribution of radiation component 52 a). Ifthe width of the smallest non-contiguous region, the bit-region (i.e.,pixel or dots), of 50 a along the azimuthal axis, Θ, is equal to or lessthan one-half the width of target image along the azimuthal axis, theintensity of the incident radiation can be modulated with threesubstantially distinct levels of contrast as zero, one, or two adjacentbit-regions (forming a second non-contiguous region with twice the areaof the bit-region) are moved under target image 52. This is analogous toa two-bit halftone, which has reflectance (or transmission) values of{0,0.5,1}. By using non-contiguous regions with smaller widths relativeto the target image width the number of substantially distinct levels ofcontrast can be increased.

As shown in FIG. 2, radiation intensity filters 50 a-50 d of modulator22A resemble concentric barcodes along the azimuthal axis, which areindividually engineered to encode a section of target image 52 as adigitized approximation or replica (e.g., a halftone representation) ofsin²(mθ) as modulator 22 is rotated about axis 40. Radiation filters 50a-50 d comprise a plurality of non-contiguous regions having opticalproperties substantially different from substrate 23, including a numberhaving a spatial extent along the azimuthal axis, Θ, which issubstantially smaller the width of the target image 52 along theazimuthal axis. As shown in FIG. 2, the total number of non-contiguousregions comprising the radiation filters of the present invention isgreater than the number of local maxima present in the substantiallysmooth function being replicated. For example, the function sin²(mθ) has2m local maxima (i.e., where sin²(mθ)=1) over the range {0,2π}, but theradiation filters of the best-mode of the present invention have aminimum of 4m non-contiguous regions of at least two different sizes,and with at least two different inter-region spacings, to provide ahalftone representation of sin²(mθ) over the same interval. The numberof levels of contrast or gray scale is substantially equal to one plusthe ratio of the target image width to the width of the smallestnon-contiguous region (e.g., the minimum feature size of the chosenlithography) along the azimuthal axis, Θ.

The modulation function of the filters on modulator 22A can change inboth the radial and azimuthal directions. In the embodiment of FIG. 2,the modulation functions of the filters 50 a-50 d change only in theazimuthal direction and not in the radial direction. Each of the filters50 a-50 d occupies a two-dimensional annular area having a substantiallyconstant radial width. The radiation filters shown in FIG. 2 modulatethe intensity of the incident radiation uniformly across the radialwidth of the encoding channel. As a result, the present invention isimmune to modulation waveform distortion resulting from arbitrary radialintensity distributions. If the target image 52 is a dispersed image,the intensities of the spectral components encoded by filters 50 a-50 dare modulated independent of the bandwidth. If the target image 52 is animage of an extended source, the intensities of the spectral componentsencoded by filters 50 a-50 d are modulated independent of the spatialresolution (or field of view) along the axis of the extended sourcewhich is projected along the radial axis of modulator 22.

In another embodiment of the invention, the “barcode” like structuresshown in 50 a-50 d, which are shown to extend continuously across theradial width of the radiation filter, are broken up to control themodulation depth and/or to increase the number of distinct levels ofcontrast available. This embodiment may be useful for improvingorthogonality or to control the modulation depth on a channel-by-channelbasis independent of the bandwidth (or field of view/field ofillumination), which may be useful for balancing signal levels insystems where one or more channels have a disproportionately largefraction of the total incident radiation. Preferably, sequential“barcode” like structures in the radiation filter will be broken up in a“checker-board” like pattern to control the modulation depth and/orincrease the number of available levels of contrast while substantiallyprecluding waveform distortion (of an encoded component) resulting fromarbitrary radial (and/or azimuthal) intensity distributions.

In the preferred embodiment, the radiation filters 50 a-50 d onmodulator 22A comprise an annular region substantially encompassing aplurality of pixels having optical characteristics substantiallydifferent from the substrate. The pixels are patterned substantiallywithin the annular region to modulate the intensity of a correspondingcomponent predominantly along an azimuthal axis to provide an encodedcomponent, wherein the amplitude of the encoded component changesbetween three or more substantially distinct levels of contrast as thesubstrate is rotated about rotation axis 40. Instead of using asubstrate with low reflectivity or transmission and a patterned layer ofhigh reflectively material on the substrate as described above, (orforming patterned transmissive areas in an opaque substrate), theradiation filters may be constructed in a different manner. Thus asubstrate with moderate reflectivity or transmission may be employedinstead. Then in areas of the filters requiring high reflectivity ortransmission, an area having such characteristics is formed (by depositof a reflective layer or formation of transmissive area), and a layer oflow reflectivity or opaque material may be deposited in areas of thefilter calling for such characteristics.

Instead of using patterns of alternating high and low reflectance ortransmission, it is also possible to construct the modulators withsubstantially orthogonal modulation functions that are not digitized butare “analog” in nature. Thus neutral density filters may be used forthis purpose, where the filters are formed by sputtering a radiationreflective material onto a non-reflective or transparent substrate.Depending on the thickness of the material sputtered (or the dopingconcentration in one or more semiconductor substrate layers; e.g., Si,Ge, GaAs), the amount of transmission or reflection can be controlled toachieve a substantially continuous and smooth intensity modulationfunction. In this embodiment, the radiation filters have substantiallycontinuously variable optical characteristics along an azimuthal axis,and the optical characteristics are continuously varied to modulate theintensity of a corresponding component as a substantially smoothfunction of a rotation angle of the modulator about the rotation axis.

FIG. 3A illustrates one possible digitized approximation 51 to thesin²(mθ+pπ/4) function with m=1 and p=0 which is obtained by roundingsin²(θ) up or down using 20 levels of contrast or gray scale. Also shownis the digitized approximation to the sin²θ with three levels of grayscale, 51×. In general, the more levels of gray scale the closer is thedigitized approximation to the idealized modulation function sin²(θ)which is shown in dotted line 50′. Obviously, other digitizedapproximations of the idealized function 50′ may be employed and arewithin the scope of the invention. The digitized approximations areadequate when it is possible to differentiate the contribution to thedetector signal caused by the various encoded components without havingto solve a simultaneous system of equations, and may include a small butfinite number of corrections to compensate for the effects ofdigitization.

FIG. 3B is a plot showing the effects of finite digitization on thenominally orthogonal amplitude wavefunctions, sin²(mθ+pπ/4). The datapoints were obtained for a twenty-five channel system, where p=0, andm=1−25. A difference in the decoded amplitudes is defined by normalizingthe twenty-five amplitudes to unity, decoding the amplitudes a firsttime, and then varying the amplitude of a single channel and decodingthe amplitudes a second time. The average output error is given by thesum of the absolute difference in the first and second decodedamplitudes divided by the number of channels. In the figure, 50E.1,50E.2 and 50E.3 are the resulting errors for varying the amplitude ofthe fundamental, m=1, the first harmonic, m=2, and the second harmonic,m=3 by ±100%. The error for varying the amplitude of the m=11 term isalso shown by 50E.11. The figure clearly illustrates the effects offinite digitization on the orthogonality of the modulationwavefunctions. Low end applications may only need 3-10 levels ofcontrast to meet a given accuracy specification, but high-end systems,where a premium is placed on photometric accuracy, may need 100 or morelevels of contrast. For the most demanding applications, the first-orderamplitude correction described below may be used to correct the decodedamplitudes for the interference.

As noted above, many of the advantages of the invention stem from thefact that it is possible to choose filter modulation functions thatretain the optimum 50% duty cycle and to decode the detector signal toobtain the respective amplitudes of two or more encoded componentswithout having to solve a simultaneous system of equations. For manyapplications, this is possible where the modulation functions areroughly orthogonal. For some applications requiring very high accuracy,it may be useful to define substantial orthogonality as follows. Themodulation functions of two radiation filters may be considered to besubstantially orthogonal to each other when changing the amplitude ofthe first (second) encoded component by 100% results in an error in thedecoded amplitude of the second (first) component of less than one partin 100 after applying the first-order amplitude correction as describedbelow.

Target Images

FIG. 4A and FIG. 4B are illustrations of target image 52 which is formedby pre-encoder optic 36A of FIG. 1A onto modulator 22 to illustrate theinvention. As noted above, the target image is either a dispersed imagewith different spectral components focused at different points along anencoding axis, or a extended image with different spatial componentsfocused at different points along an encoding axis. For simplicity, onlyfilters 50 a and 50 b of FIG. 2 are shown schematically in FIG. 4A andFIG. 4B. Preferably, as shown in FIG. 4, the encoding axis issubstantially along the radial axis, R, of modulator 22. The targetimage width is defined as the spatial extent perpendicular to theencoding axis.

In FIG. 4A we illustrate the case where target image 52 is a dispersedimage of a broadband or multiple wavelength source with its dispersionaxis along the radial axis, R. Two different spectral components, 52 aand 52 b, which are encoded by modulator 22B, are shown by differentcrosshatching in FIG. 4A. Spectral component 52 a is characterized by acenter wavelength (λ₂+λ₁)/2 and a bandwidth (λ₂−λ₁). Similarly, spectralcomponent 52 b is characterized by a center wavelength (λ₄+λ₃)/2 and abandwidth (λ₄−λ₃). Examples of broadband or multiple wavelengthradiation sources include blackbody radiators, incandescent lamps,light-emitting diodes, low-pressure gas lamps, optically, biologicallyor chemically excited samples, fluorescent-labeled beads dispersed in afluid, dye lasers, semiconductor lasers, glass lasers, gas lasers,multi-wavelength optical fibers, hot gas and/or vapor streams, furnaces,plasmas, corona discharges, atomic emissions, and reflected or filteredsunlight.

In FIG. 4B we illustrate the case where target image 52 is an extendedimage (i.e., the image of an extended source). In this case we simplifyidentify 52 a and 52 b as two different spatial components of theextended source and S1 and S2 define the spatial boundaries (i.e., thefield of view) of 52 a, and s₃ and s₄ define the spatial boundaries(i.e., the field of view) of 52 b. One example of an extended source isa collection of different samples which emit, scatter, transmit orreflect radiation in response to an excitation. In this case, thespatial components 52 a and 52 b correspond to the radiation emitted,scattered, transmitted or reflected by a particular sample in thecollection. A second example of an extended source is a linear array ofoptical fibers. In this case, the spatial components 52 a and 52 bcorrespond to the radiation emitted or reflected by a particular fiberin the array. A third example of an extended source is radiationtransmitted through a collection of bandpass filters and/or dichroicmirrors, a linear variable filter, or a collection of correlationradiometry cells. In this case, spatial components 52 a and 52 bcorrespond to radiation transmitted through or reflected from twodifferent bandpass filters in the collection or two different portionsof the linear variable filter (or two different correlation radiometrycells). A fourth example of an extended source is a collection ofradiation sources, (e.g., a linear array light emitting diodes or laserdiodes). In this case, the spatial components 52 a and 52 b correspondto the radiation emitted by the individual sources comprising thecollection. A fifth example of an extended source is one or moreexcitation sources combined with one or more refractive or reflectiveoptical elements (e.g., a series of beam splitters) to produce aplurality of substantially identical sub-images. Other examples ofextended sources include semiconductor wafers and circuits, mechanicalassemblies, a multi-mode optical fiber, a multi-lane electrophoresis, aninterference pattern (e.g., one or more excitation sources combined witha diffractive optic to produce multiple sub-images of each excitationsource), and reflected or filtered sunlight collected over an extendedarea.

Decoding Algorithm

At any given rotation angle, the total signal incident on detector 26 inFIG. 1A is given by the sum of the sub-signals arising from the selectedradiation components, 52 a-52 d, independently encoded by theangle-dependent reflectance of their corresponding radiation filters, 50a-50 d, on modulator 22. In general, the radiation filters can bedefined by specifying the values for m and p in the expressionsin²(mθ+pπ/4), where m is an integer or half-integer. Thus in general,the intensity of the encoded beam detected by detector 26 in FIG. 1Afrom a radiation modulator such as modulators 22A or other modulatorsdescribed in this application can be given in general by the followingequation:

$\begin{matrix}{{S(\theta)} = {\sum\limits_{m}{\sum\limits_{p}{a_{m,p}{\sin^{2}\left( {{m\;\theta} + \frac{p\;\pi}{4}} \right)}}}}} & (1)\end{matrix}$where S(θ) is the intensity detected by the detector 26, and thesummations include all of the m and p values corresponding to thefilters present in a given modulator design. In equation (1), a_(m,p) isthe amplitude of the encoded component that has been encoded by theradiation filter having a modulation function which is a digitizedapproximation or replica (e.g., a halftone representation) ofsin²(mθ+pπ/4). This invention permits one to retain the optimum 50% dutycycle and to determine the amplitudes of the encoded components withoutsolving a simultaneous system of equations for encoding channels havingarbitrary radial width and target images having arbitrary radialintensity distributions. In the summation process in equation (1), thefilters present in a particular modulator may not include filterscorresponding to all combinations of m and p values. This is exemplifiedin the modulator 22A of FIG. 2 where p takes on only the value 0, and inthe modulator 22B of FIG. 5 where m takes on the value 3 throughout allthe filters. In such event, the amplitude a_(m,p) for filters that arenot present in the modulator is simply 0. Preferable, decoding algorithm28.dec is provided with a list of the m and p values patterned onto themodulator and the summation in equation (1) is restricted to the list.More preferably, the list is encoded onto the disc so that the correctlist is always used by 28.dec to decode the detector signal.

As a further benefit, the present invention enables the use ofgeneralized approaches for the modulator drive system, data acquisitionand the decoding algorithms. For example, motorized spindle 42 isrotated at a roughly constant frequency (as opposed to being stepped),the detectors analog output is sampled by Analog-to-Digital Converter(ADC) 28.adc which is triggered by optical switch 70 in response totiming marks 60. Optical switch 71 responding to timing mark(s) atnon-regular angular intervals 61, provides computer 28 with a referenceof 0 degrees to synchronize the output of 28.adc with the decodingalgorithm 28.dec. Hence, the decoding algorithm is compatible with anyfunction defined in equation (1), and the number and identity {m,p} ofthe modulated components, and the specific analytic functions to beperformed on the decoded data are defined in application specificsoftware. Preferably, the list of {m,p} values corresponding to theradiation filters on the modulator are encoded onto the disc.

If p and q are integers, the trigonometric functions sin²(mθ+pπ/4) obeythe following orthonormal relation.

$\begin{matrix}{{\int_{0}^{2\;\pi}{{\mathbb{d}\theta}\;{\cos\left( {{2\; m\;\theta} + \frac{p\;\pi}{2}} \right)}{\sin^{2}\left( {{n\;\theta} + \frac{q\;\pi}{4}} \right)}}} = {{- \frac{\pi}{2}}{\delta_{m,n}\left( {\delta_{p,q} - \delta_{p,{q \pm 2}}} \right)}}} & (2)\end{matrix}$The amplitudes a_(m,p) of the encoded spectral components may bedetermined using the orthogonal properties of the trigonometricfunctions in accordance with equation (3) below:

$\begin{matrix}{a_{m,p} = {{- \frac{2}{\pi}}{\int_{0}^{2\;\pi}{{\mathbb{d}\theta}\;{\cos\left( {{2\; m\;\theta} + \frac{p\;\pi}{2}} \right)}{S(\theta)}}}}} & (3)\end{matrix}$

First-Order Amplitude Correction

One complication introduced by the use of digitized approximations orreplicas of the trigonometric functions sin²(mθ+pπ/4), is that theorthogonality described by equation (2) and used in equation (3) aboveis inexact. As a result, in some applications it may be necessary forthe interference terms to be accounted for and the individual amplitudescorrected for the interference resulting from the other channels, whichnaturally leads to a series of successively higher-order correctionterms:a _(m,p) =a _(m,p) ⁽⁰⁾ +a _(m,p) ⁽¹⁾+  (4)where the zero-order amplitude coefficients are determined from

$\begin{matrix}{a_{m,p}^{(0)} = {{- \frac{2}{\pi}}{\int_{0}^{2\;\pi}{{\mathbb{d}\theta}\;{\cos\left( {{2\; m\;\theta} + \frac{p\;\pi}{2}} \right)}{S(\theta)}}}}} & (5)\end{matrix}$The first-order amplitude correction is given by

$\begin{matrix}{a_{m,p}^{(1)} = {\sum\limits_{n}{\sum\limits_{q}{A_{m,p}^{n,q}a_{n,q}^{(0)}}}}} & (6)\end{matrix}$where it is understood that in the summation over patterned radiationfilters, the term where n=m and q=p is excluded.

In equation (6), the matrix elements are determined by sequentiallydecreasing or enhancing the amplitudes of the a_(n,q) and measuring thechanges in a_(m,p) ⁽⁰⁾. For example, if we identify δa_(m,p) ⁽⁰⁾ as theobserved change in a_(m,p) ⁽⁰⁾ resulting from a_(m,p) ⁽⁰⁾, the imposedchange on a_(n,q) ⁽⁰⁾, the corresponding matrix element is given by

$\begin{matrix}{A_{m,p}^{n,q} = \frac{\delta\; a_{m,p}^{(0)}}{\Delta\; a_{n,q}^{(0)}}} & (7)\end{matrix}$

Preferably, the imposed change on a_(n,q) ⁽⁰⁾ is facilitated by amovable mask having an aperture or obscuration which is comparable insize to the radial width of the radiation filters, where the mask istranslated along the radial axis of modulator 22 such that the incidentradiation is selectively transmitted or blocked from the radiationfilters in sequence. For example, a disc with a spiral aperture orobscuration which is mounted in a plane parallel to modulator 22,directly above or below modulator 22, and is stepped about rotation axis40. More preferably, the imposed change on a_(n,q) ⁽⁰⁾ is facilitated bya dedicated radiation source and detector, which are independently orcollectively translated along the radial axis of modulator 22 such thatthe incident radiation is selectively modulated by the radiation filtersin sequence. Most preferably, the beam size of the dedicated radiationsource along the radial axis is substantially smaller than the radialwidth of the narrowest radiation filter on modulator 22. In this manner,the modulated components can be isolated from one another to moreaccurately determine their respective harmonic contents. Such a devicefor illuminating and/or isolating specific radiation filters can also beused to produce a known encoding signal for the Secondary Encoder TimingSignal Synchronization described below.

In practice, the integral shown in equation (5) is replaced with adiscrete summation over M, the number of Data Acquisition (DAQ) events(or intervals, steps or cycles) per rotation. On start-up, a set ofdecoding coefficients (e.g., a trigonometric look-up table), is definedand initialized with the values of cos(2mθ+pπ/2) evaluated at the DAQintervals for rotation

$\begin{matrix}{T_{m,p}^{j} \equiv {{- \frac{2}{\pi\; M}}{\cos\left( {\frac{4\; j\; m\;\pi}{M} + \frac{p\;\pi}{2}} \right)}}} & (8)\end{matrix}$The zeroth-order amplitude coefficients are given by a summation of thediscrete signal measurements multiplied by the corresponding decodingcoefficients

$\begin{matrix}{a_{m,p}^{(0)} = {\sum\limits_{j = 1}^{M}{T_{m,p}^{j}{S(j)}}}} & (9)\end{matrix}$where S(j) is the ADC reading from the detector at the jth DAQ step;i.e., the output from 28.adc. At the end of a complete rotation, thefirst-order amplitude corrections are evaluated if necessary for a givenapplication:

$\begin{matrix}{a_{m,p}^{(1)} = {\sum\limits_{n}{\sum\limits_{q}{A_{m,p}^{n,q}a_{n,q}^{(0)}}}}} & (10)\end{matrix}$where it is understood that the term in the summation where n=m and q=pis excluded. Note that if the amplitudes have not changed significantlysince the last time the corrections were evaluated, the corrections neednot be re-evaluated.

Transient Signal Detection

Preferably, computer 28 in FIG. 1 includes a Transient Signal Algorithm,28.utl(TSA) to detect transients in the amplitudes of the encodedcomponents that occur during a rotational period of modulator 22. Morepreferably, the computer will analyze the transient signal to determineits harmonic content. At each DAQ step j, 28.utl(TSA) subtracts thedetector signal from one or more previous detector signals or theexpected signal calculated using the last calculated zeroth-orderamplitude coefficients defined by equation (9) above:

$\begin{matrix}{{\Delta\;{S^{k}(j)}} = {{S^{k}(j)} - \left\{ {\sum\limits_{m}{\sum\limits_{p}{a_{m,p}^{({k - 1})}{\sin^{2}\left( {\frac{2\; j\; m\;\pi}{M} + \frac{p\;\pi}{4}} \right)}}}} \right\}}} & (11)\end{matrix}$

where S^(k)(j) is the output from 28.adc (i.e., the detector signal)measured at the jth step on the kth rotational period and the a_(m,p)^((k−1)) are the zeroth-order amplitude coefficients calculated for the(k−1)th rotational period. The magnitude of ΔS^(k)(j) is used to detectamplitude transients in one or more encoded components that occur on asub-rotational-period time scale. Preferably, when the magnitude ofΔS^(k)(j) exceeds a predefined threshold, 28.utl(TSA) directs theanalyzers operating system to increase the speed of the motorizedspindle 42, and when the magnitude of ΔS^(k)(j) drops below a secondpredefined threshold for a predefined extended period of time,28.utl(TSA) directs the analyzers operating system to decrease the speedof the motorized spindle 42. In that way, the motorized spindle 42 canbe run a slow as possible, thereby increasing the operating life. Mostpreferably, ΔS^(k)(j) is analyzed by 28.utl(TSA) over a sufficientnumber of DAQ cycles to determine its harmonic content, which in turnwill be used as input by the decoding algorithm to compensate for theharmonic interference resulting from sub-period signal transients.Control of motorized spindle 42 may be accomplished by means of28.utl(MCA) and 28.dac via a control signal line to motorized spindle42.

Modulator Patterns

FIG. 5 is a top view of a radiation modulator 22B to illustrate anotheraspect of the invention. Modulator 22B is provided with four radiationfilters 50.5, 50.6, 50.7 and 50.8, where the modulation functions of thefour filters are all digitized approximations of the function of thegeneral form sin²(mθ+pπ/4) described above in reference to modulator 22Aof FIG. 2. In modulator 22B of FIG. 5, radiation filters 50.5 and 50.6both have m values of 3, but p values of 0 and 1, respectively.Similarly, filters 50.7 and 50.8 both have m values of 5, but p valuesof 0 and 1, respectively. By inspection of the orthogonality relationdefined in equation (2), it is clear that all four radiation filters onmodulator 22B are substantially orthogonal to one another. The highestharmonic (m value) that can be patterned on modulator 22 is governed bythe width of target image 52 along the azimuthal axis and thecircumference of modulator 22 at the chosen radius. By using filterpairs with the same m values but having p values that differ by an oddinteger, the number of orthogonal filters up to any given harmonic canbe doubled.

FIG. 6 is a top view of a radiation modulator 22C to illustrate anotheraspect of the invention. Modulator 22C is patterned with four radiationfilters, 50.9, 50.10, 50.11 and 50.12, having the same modulationfunction (i.e., sin²(mθ+pπ/4) with identical m and p values), butlocated at different radii from the rotational axis 40 and separatedfrom one another for encoding different radiation components. In thismanner, groups of non-contiguous radiation components can becollectively modulated to enhance the signal-to-noise ratio of theanalyzer.

FIG. 7 is a top view of a radiation modulator 22D to illustrate anotheraspect of the invention. Modulator 22D is patterned with two radiationfilter pairs, 55.1 comprising radiation filters {50.13,50.14}, and 55.2comprising radiation filters {50.15,50.16}, and a single non-pairedradiation filter 50.17. In modulator 22D, filter pairs 55.1 and 55.2 aredesigned to measure the difference in radiation intensity incident onthe two filters comprising the pair, {50.13,50.14} and {50.15,50.16},respectively. The modulation functions of the filters comprising eachfilter pair are complementary or out of phase so that the amplitude andphase of the encoded component are determined by the relative proportionof radiation incident on the two filters. In modulator 22D, themodulation functions of the filters are all digitized approximations ofthe general form sin²(mθ+pπ/4). For modulation functions of the formsin²(mθ+pπ/4), the complementary configuration is where both filterscomprising the pair have the same m value, but different p values, wherethe difference in p values is an even integer.

In reference to 55.1 of FIG. 7, filters 50.13 and 50.14 are adjacent toone another. In this manner, the resulting signal from 55.1 issubstantially equivalent to the derivative of the intensity distributionwith respect to radial position evaluated at the border radius, BR.1. Inone embodiment, the amplitude of the encoded component resulting fromfilter pair 50.17 is nulled or zeroed by balancing the intensity of theradiation which is incident on 50.13 and 50.14.

In reference to 55.2 in FIG. 7, filters 50.15 and 50.16 are separatedfrom one another along the radial axis. The amplitude and phase of theresulting encoded component is determined by the relative proportion ofthe radiation incident on the two filters. In this manner, thedifference in intensity of two radiation components which are separatedalong the radial axis can be measured directly. In many applications,analytical function 28.asf normalizes one or more intensity differencesby a corresponding absolute intensity. In modulator 22D, filter 50.17 isdesigned to provide the absolute intensity at the midpoint between 50.15and 50.16. The modulation frequency (m value) of 50.17 is chosen to bemuch higher than the modulation frequency of 55.2 so that the signaloriginating from 50.17 can be filtered out using an appropriateelectronic bandpass filter 28.bpf between the detector 26 and the analogto digital converter 28.adc. Preferably, the electronic bandpass filter28.bpf in FIG. 1 has a programmable passband such that the signaloriginating from 50.17 can be switched in and out of the signal path to28.adc as needed. In this manner, the absolute intensity of radiationencoded by filter 50.17 can be measured during a calibration cycle andsubsequently, used to normalize the intensity difference encoded bycomplementary pair 55.2 (e.g., to enhance the instruments speed,resolution, and/or preserve the dynamic range of 28.adc). In thealternative, the signal from detector 26 can be split into two signalpaths with different electronic bandpass filter, and a first ADC can beused to measure the component encoded by 55.2 and a second ADC can beused to measure the component encoded by 50.17.

FIG. 8 is a top view of a radiation modulator 22E to illustrate anotheraspect of the invention. Modulator 22E is provided with two radiationfilter pairs, 55.3 and 55.4, for measuring the difference in theradiation intensity incident on the two filters comprising the pair.Modulator 22E is also provided with two non-paired radiation filters,50.22 and 50.23, for measuring the sum of the radiation intensityincident on the annular region encompassing 55.3 and 55.4, respectively.The encoded components resulting from 55.3 and 55.4 are orthogonal toone another, and the encoded components resulting from 50.22 and 50.23are also orthogonal to one another. In FIG. 8, 55.3 and 50.22 occupydifferent annular segments of the same annular region, with 55.3occupying the upper half of modulator 22E (i.e., the annular segmentbetween 0 and 180 degrees), and 50.22 occupying the lower half ofmodulator 22E (i.e., the annular segment between 180 and 360 degrees).Similarly, 55.4 and 50.23 occupy different annular segments of the sameannular region, with 55.4 occupying the upper half of the modulator 22Eand 50.23 occupying the lower half of the modulator. As modulator 22E isrotated counter-clockwise, the target image 52 is encoded by 55.3 and55.4 for the first half period of rotation and by 50.22 and 50.23 forthe second half period of rotation. Preferably, computer 28 usessub-signal separator algorithm 28.sss to separate the detector signalinto two sub-signals corresponding to {55.3,55.4} and {50.22,50.23},respectively. These two sub-signals would be processed by decodingalgorithm 28.dec to determine the amplitudes of the encoded components.More preferably, the two filter pairs (55.3 and 55.4) and the twonon-paired radiation filters (50.22 and 50.23) are each encoded withunique encoding functions to provide four substantially orthogonalencoded components with 25% duty cycles. In this manner, both thederivative of the intensity distribution with respect to radial positionevaluated at the border radius and the total intensity of each encodedradiation component can be measured substantially simultaneously.Modulator 22E incorporates a special case of modulation functions basedon one or more incomplete rotation periods of modulator 22 (seedescription below).

The configuration of the annular regions, annular segments, and theradiation filters and filter pairs of modulator 22E where chosen forillustrative purposes, and are not meant to limit the scope of theinvention. Other configurations that contain different annular regions,different annular segments, different radial positions, and/or radialwidths for the radiation filters and filter pairs are within the scopeof the invention.

Alignment Calibration and Tracking Analyzer

FIG. 9A is a schematic illustration of the effect of moving one or moreelements of pre-encoder optic 36A on the focus and position of targetimage 52 on modulator 22. For brevity we define the “alignment of targetimage 52 onto modulator 22” to include both i) the focus of target image52 onto the surface of substrate 23, and ii) the position of targetimage 52 onto modulator 22. Thus, as shown in FIG. 9A, when foldingmirror 34 is in position 34(1), target image 52′ is not properlyaligned, but when folding mirror 34 is in position 34(2), target image52 is properly aligned on the surface of modulator 22. An unwantedchange in the alignment of target image 52 on the surface of modulator22 can be caused by expansions or contractions of the various componentsand mounting fixtures of 36A in response to changes in ambienttemperature. Another cause for the misalignment of target image 52 onthe surface of modulator 22 is the change in modulator radius as afunction of temperature.

In another embodiment of analyzer 100, Alignment Calibration andTracking Analyzer, the position of one or more optical elements may becontrolled to correct alignment errors in the system. For this purpose,the folding mirror 34 is mounted on a movable stage. Preferably, themovable stage controlled by one or more actuators driven by 28.dac formoving the folding mirror to position 34(2), so that target image 52 isproperly aligned on modulator 22.

FIG. 9B is a schematic view of Alignment Calibration and TrackingAnalyzer where the position of folding mirror 34 is controlled bymovable stage 35. Preferably, movable stage 35 incorporates one or moreactuators to translate folding mirror 34 along one or more axes. Morepreferably, movable stage 35 incorporates two or more actuators totranslate and/or rotate folding mirror 34 along and/or about one or moreaxes. In this manner, with appropriate control signals, moveable stage35 can be used to position folding mirror 34 in order to properly aligntarget image 52 onto modulator 22.

The Alignment Calibration Mechanism comprises the decoded amplitudes andphases of one or more alignment components (or channels), AlignmentCalibration Algorithm 28.utl(ACA), one or more calibration curvesrelating the decoded amplitudes to the alignment of target image 52 onmodulator 22, digital-to-analog converter 28.dac, voltage-controlledmovable stage 35, and folding mirror 34.

The Alignment Tracking Mechanism comprises timing marks 60, and 61and/or alignment marks 62, alignment probe 72, Alignment TrackingAlgorithm 28.utl(ATA), hardware driver 28.drv, movable stage 35, andfolding mirror 34. Preferably, folding mirror 34 is mounted on moveablestage 35 that incorporates one or more actuators to position foldingmirror 34 to properly align target image 52 onto modulator 22.

The input for alignment tracking algorithm 28.utl(ATA) is the output ofalignment probe 72 in response to timing/location marks 60, 61, and/or62 (or more preferably, one or more complementary filter pairs describedbelow), and the rotation of modulator 22. The alignment trackingalgorithm 28.utl(ATA) analyzes the output of alignment probe 72 todetect spindle wobble, vibration or a misaligned modulator 22 onsubstrate 23. Preferably, alignment tracking algorithm 28.utl(ATA)generates (or calculates) one or more tracking coefficients which arethen used by application specific function 28.asf to compensate for thedetected spindle wobble, vibration or a misaligned modulator 22 onsubstrate 23. More preferably, alignment tracking algorithm 28.utl(ATA)generates a control signal for movable stage 35 to dynamically positionfold mirror 34 (and/or other optical elements) to keep target image 52properly aligned. Most preferably, the output of 28.utl(ATA) can be usedto provide feedback to an assembly technician during the manufacturingprocess. In this manner, the concentricity of the encoding pattern onmodulator 22 with respect to axis of rotation 40 may be optimized to thepoint where subsequent alignment tracking becomes unnecessary for agiven application.

The input for alignment calibration algorithm 28.utl(ACA) is the decodedamplitudes of one or more alignment components. Dedicated filters andcomplementary filter pairs organized into one or more alignment channelscan be used in the analyzer depicted in FIG. 9 for alignment purposes.FIG. 9C illustrates one possible embodiment of modulator 22 withradiation filters and filter pairs comprising two signal channels andtwo alignment channels. In modulator 22F, the radial position ofradiation filter 50.24 and 50.25 correspond to the nominal radialposition of two expected alignment components in target image 52.Examples of alignment components include: the sub-images of two or morediscrete fluorescent samples, dedicated reference fibers in an opticalfiber array, dispersed or filtered spectral features of a sample, anddispersed or filtered spectral features in one or more optical elements(e.g., the edge of a filter). Radiation filters 50.24 and 50.25 arebounded by radiation filter pairs 55.5 and 55.6, respectively. Radiationfilter pairs 55.5 and 55.6 are comprised of radiation filters withcomplementary (e.g., 180 degrees out of phase) modulation functions sothat the amplitude and phase of the resulting encoded alignmentcomponent is determined by the relative proportion of radiation incidenton the two filters. Preferably, the position and radial width of thefilters comprising 55.5 and 55.6 are engineered to produce acharacteristic amplitude and phase in the two encoded alignmentcomponents when target image 52 is properly aligned on modulator 22F.Most preferably, when target image 52 is properly aligned the intensitydistributions across 55.5 and 55.6 zeros the amplitude of the encodedalignment components. Any error in the alignment of target image 52results in a characteristic amplitude and phase in one or more of theencoded alignment components. In this manner, a the signals in 55.5 and55.6 provide calibration data on the magnitude and direction of thefocus error and position error of target image 52 on substrate 23 andmodulator 22F, respectively. Preferably, one or more calibration curvesare generated by precisely detuning the focus and position of targetimage 52 onto substrate 23 and modulator 22F, respectively, (e.g., usingmovable stage 35) and recording the resulting amplitude and phase of theencoded alignment components. More preferably, alignment calibrationalgorithm 28.utl(ACA) inputs the amplitudes and phases of the currentalignment components and uses the calibration curves to generate one ormore calibration coefficients which are then used by applicationspecific function 28.asf to compensate for the effects of the alignmenterror. Most preferably, 28.utl(ACA) compares the current alignment tothe calibration curves to generate a control signal for moveable stage35 to position fold mirror 34 (and/or other optical elements) to keeptarget image 52 properly aligned. The output of the alignmentcalibration algorithm 28.utl(ACA) can also be used to provide feedbackto an assembly technician during the manufacturing process. A properalignment of target image 52 along the azimuthal axis of modulator 22can be obtained by simply maximizing the amplitude of the encodedcomponents resulting from 50.24 and 50.25.

The shared components of the Alignment Calibration Mechanism and theAlignment Tracking Mechanism shown in FIG. 9B were chosen forillustrative purposes and are not meant to limit the scope of theinvention. Other configurations which utilize independent (or multipleindependent) input sources, hardware drivers, movable stages, actuators,and optical components are within the scope of the invention. In thepreceding description, folding mirror 34 was chosen for illustrativepurposes, it being understood that the position of other opticalelements, including various combinations of entrance aperture 32, exitaperture 44, pre-encoder optic 36A, post-encoder optic 36B, detector 26,and modulator 22, could be controlled for alignment purposes, and arewithin the scope of the invention. The radiation filters used inmodulator 22F were chosen for illustrative purposes, it being understoodthat other filter pair and filter combinations are useful for alignmentpurposes and are within the scope of the invention. In particular,various aspects of the modulators 22D and 22E shown in FIG. 7 and FIG.8, respectively are useful for alignment purposes. The calibration andalignment mechanisms described above are applicable to all of theembodiments of the present invention.

Interlaced Excitation Analyzer 300

In some applications, it may be desirable to measure a samples responseto two or more different components of excitation radiation. Examples ofcomponents of excitation radiation include a collection of differentlasers, a multi-line laser or low-pressure gas lamp combined with adiffractive or refractive optic to separate the emission lines, opticalfibers, or lamp/filter combinations. Examples of samples include amulti-lane/multi-capillary electrophoresis, and a collection of distinctfluorescence emitting (or Raman scattering) samples arranged in a lineararray. Such and other examples of excitation components and samples arewithin the scope of the invention. In some instances, it may also bedesirable to measure a samples response to two or more differentexcitation components substantially simultaneously. For example, somesamples are altered by the excitation radiation such that the results ofa sequence of excitation/response measurements may differ depending uponthe order of the applied excitation components. Another example is asample that is flowing in a process stream (e.g., electrophoresis, flowcytometry, water, or natural gas) where the dwell time at the locationof the measurement is insufficient to make the excitation measurementsin series. Another example is the excitation analysis of samplesundergoing chemical kinetics. The interlaced excitation analyzerdescribed below, and shown in FIG. 10, permits the emitted, scattered,transmitted or reflected radiation from a sample in response to two ormore different excitation components to be detected substantiallysimultaneously.

FIG. 10A is a schematic view of analyzer 300, which comprises analyzer100 of FIG. 1 and an interlacing mechanism to excite a radiationemitting sample with two or more distinct components of excitationradiation substantially simultaneously. In FIG. 10A, one or moreexcitation sources (not shown) provides excitation radiation comprisingtwo distinct excitation components, EX1 and EX2. In analyzer 300,excitation components EX1 and EX2 are directed to sample 324substantially in sequence (e.g., interlaced) along optical paths P1 andP2 as modulator 322 is rotated about rotation axis 340. Preferably, theexcitation sequence substantially precludes more than one of theexcitation components from reaching the sample 324 at any given time.Preferably, a variable attenuator may be used to precondition or presetthe intensities of the excitation components. In response to the encodedexcitation beam, sample 324 emits, transmits, reflects or scatters aresponse beam of radiation, which comprises at least two responsecomponents. The response beam is imaged by pre-encoder optic 36A to forma target image 352 with response components focused at substantiallydifferent points along the radial axis on modulator 322. Modulator 322has at least two radiation filters at different radii from the rotationaxis 340 for encoding the response components to provide an encodedresponse beam. Preferably, target image 352 is aligned with theradiation filters such that the encoded components have a substantiallyone to one correspondence with the response components. Preferably, theamplitudes of the encoded response components are substantially smoothfunctions or change between three or more substantially distinct levelsof contrast as modulator 322 is rotated about the rotation axis 340.More preferably, the amplitudes of the encoded response components aresubstantially orthogonal to one another. Most preferably, the amplitudesof the encoded response components are all digitized approximations ofthe general form sin²(mθ+pπ/4). The encoded response beam is collected,directed and focused by post-encoder optic 36B onto detector 26. Inresponse to the encoded response beam, detector 26 provides an output tothe analog-to-digital converter (ADC) 28.adc on computer 28. As shown inFIG. 1A, Computer 28 includes a sub-signal separator algorithm 28.sss ,which is used by analyzer 300 to separate the time-based signalgenerated by detector 26 in response to the encoded response beam intotwo sub-signals which correspond to the encoded response beam resultingfrom EX1 or EX2, respectively. The sub-signals are then independentlyanalyzed by decoding algorithm 28.dec to provide the amplitudes of theencoded response as a function of the excitation components.

If sample 324 is a single sample with a plurality of selected responsecomponents, analyzer 300 allows one to measure substantially theselected response components as a function of the excitation componentssubstantially simultaneously. If sample 324 is a collection of samplesand the response components are spatial components which also containspectral information of interest (e.g., a multi-lane, multi-dyeelectrophoresis or multi-dye fluorescent assay), the spectral propertiesof the response components can be determined by inserting a spectrometeror other wavelength filtering device between optical element 36B anddetector 26 and scanning the wavelength of the radiation transmitted todetector 26. More preferably, a spectrograph or otherwavelength-separating device is used to direct a number of selectedspectral components of the encoded beam to an equal number of detectors.Most preferably, computer 28 would include a sufficient number ofanalog-to-digital converters (ADCs) and decoding algorithms 28.dec suchthat the signals generated by the detectors in response to the encodedbeam could be analyzed substantially simultaneously.

FIG. 10B illustrates one possible embodiment of modulator 22 for usewith analyzer 300. Modulator 322 includes a series of staggered opticalgates 64.1 and 64.2 centered at R1 and R2, respectively. 64.1 and 64.2alternately permit the transmission of radiation components EX1 or EX2,such that radiation from only one of the excitation components isincident on the sample 324 at any given time. Preferably, the staggeredoptical gates have the same resolution as timing marks 60, where everyother gate is open, and the relative phase of the open gates in the twoannular regions are such that only one gate is open at a time. The gatesmay simply be transmissive areas in an opaque substrate or reflectiveareas in a non-reflective or transparent substrate. The response beam ofradiation is collected and focused to form a target image 352substantially along a radial axis of modulator 322 such that theresponse components are focused at substantially different points alongthe radial axis of modulator 322. The response components are encoded bythe four spatial radiation filters, 50.26, 50.27, 50.28 and 50.29 onmodulator 322 to provide an encoded response beam. Preferably, each ofthe modulation functions of 322 used to encode the response beam is asmooth function or a digitized replica of a smooth function having threeor more distinct levels of contrast as modulator 322 is rotated aboutrotation axis 340. More preferably, the amplitudes of the encodedresponse components are substantially orthogonal to one another. Mostpreferably, the encoded response components are modulated substantiallyaccording to functions of the form sin²(mθ+pπ/4).

In FIG. 10A and FIG. 10B, the optical geometry and the number ofexcitation components and encoding radiation filters was chosen forclarity, it being understood that arbitrary numbers of excitationcomponents and radiation filters are within the scope of the invention.Other optical geometries which involve separate, more elaborate opticalelements or optical system to collect and focus the input radiation ontomodulator 322 and to collect and focus the encoded beam from modulator322 onto detector 26 may be used instead in each of the embodimentsherein and such variations are within the scope of the invention. Thetransmission mode of modulator 322 was chosen for clarity, it beingunderstood that a similar device with a reflective modulator is withinthe scope of the invention.

In FIG. 10A and FIG. 10B, staggered optical gates, 64.1 and 64.2, ofmodulator 322 are used to direct the excitation components to sample 324in an interlaced sequence. This interlacing mechanism could be replacedwith by an interlaced sequence of control signals (not shown) fromcomputer 28 to one or more controllable gating devices which direct theexcitation components to 324. Examples of controllable gating devicesinclude addressable optical shutters, movable mirrors and controllablepower supplies. In this case, computer 28 would produce a sequence ofcontrol signals to a number of controllable gating sources in responseto one or more optical switches (e.g., optical switch 70, 71, and/or 72)to direct the excitation components to sample 324 substantially insequence.

In reference to FIG. 9, for analyzer 300 described above, the positionone or more optical elements can be controlled to align target image 352onto modulator 322. Preferably, sample 324 includes a number ofalignment components (e.g., one or more known fluorescent species, oneor more light-emitting diodes, or one or more optical fibers with knowspectral output distributed at known spatial positions within 324) andmodulator 322 includes a number of alignment channels to provide inputto the alignment calibration algorithm 28.utl(ACA). Preferably,28.utl(ACA) generates one or more calibration coefficients which arethen used by application specific function 28.asf to compensate for theeffects of the alignment error. More preferably, 28.utl(ACA) generatesone or more control signals to position one or more optical elements toproperly align target image 352 onto modulator 322. More preferably, thealignment spatial components would also have known spectralexcitation/emission properties for calibrating the wavelength-filteringdevice or the wavelength-separating device.

Harmonics of Incomplete Rotation Periods

The encoding functions used in modulators 22A-22D are harmonics of thecomplete rotational period of substrate 23. In other embodiments,harmonics of incomplete rotational periods (e.g., radiation filtersconfined to an annular segment within an annular region) may be usefulfor eliminating various hardware items, freeing up micro-processorresources, synchronizing the movements of external mechanical devices,measuring the position and intensity of an intensity distribution, andincreasing the spatial or spectral resolution of the analyzer. For thediscussions that follow, we define harmonics of incomplete rotationalperiods to include encoding functions derived from radiation filterswith substantially repeating patterns that have an integer number ofperiods (or half-periods) within a bounding annular segment. The generalform for the harmonics of incomplete rotation periods is given bysin²(mθ′+pπ/4), where θ′ is the compressed angle relating the azimuthallength of the annular segment to the complete period of rotation ofmodulator 22. Modulator 22E of FIG. 8 is an example of using modulationfunctions based on two incomplete rotation periods to measure both theintensity and radial position (or intensity derivative along the radialaxis of modulator 22E) of an imaged radiation distribution, therebyenhancing the measurement capability of analyzer 100. In the exampleshown in FIG. 8, the angle θ′ is compressed by a factor of two as theannular segments are one-half the rotation period of modulator 22E.

In another embodiment of modulator 22, harmonics of an incompleterotation period may be used to eliminate timing mark(s) 61 on modulator22 and optical switch 71, by replacing the signal from optical switch 71with a simple time-out on the signal originating from optical switch 70.FIG. 11A is a top view of radiation modulator which incorporatesradiation filters which are based on harmonics of an incompleterotational period. As shown in FIG. 11, radiation modulator 22DZ hasfour radiation filters, 50.30, 50.31, 50.32 and 50.33, which areharmonics of the incomplete rotation period which starts at the rotationangle θ_(i) and ends at the rotation angle θ_(f) (i.e., θ_(i) and θ_(f)define the annular segments within the corresponding annular regionsencompassing 50.30, 50.31, 50.32 and 50.33). Between θ_(f) and θ_(i),modulator 22DZ includes a passive area that is void of the radiationfilters. For clarity, we define the active period as the fraction of acomplete rotation period where target image 52 is being modulated by theradiation filters on modulator 22, and we define the passive period asthe fraction of a complete rotation period where target image 52 is notbeing modulated by the radiation filters on modulator 22. Preferably,the timing marks 60 on modulator 22DZ are patterned such that during thepassive period no ADC trigger events are generated by optical switch 70.

To use modulator 22DZ, the decoding algorithm 28.dec of radiationanalyzer 100 would be modified to eliminate the input from opticalswitch 71 and include a timer which would provide a basis for measuringthe elapsed time between ADC trigger events generated by optical switch70 in response to timing marks 60. The elapsed time between ADC triggerevents would be used to compute an average ADC trigger event period.Decoding algorithm 28.dec would include an function which would generatean ADC time-out event when the time elapsed since the last ADC triggerevent is substantially greater than the average ADC trigger eventperiod. Preferably, modulator 22DZ is patterned such that the ADCtime-out event occurs during the passive period. The ADC time-out eventis used by computer 28 to synchronize decoding algorithm 28.dec with theoutput from 28.adc. In this manner, the cost and complexity of radiationanalyzer 100 is substantially reduced.

Harmonics of an incomplete rotation period in conjunction with a passiveperiod may also be necessary when a computer-time-intensive algorithm isexecuted once per rotation period and would otherwise compromise thedata collection and decoding efforts. For example, in analyzer 100 thedata is acquired during an incomplete rotation period and theapplication-specific algorithm 28.asf is executed during the passiveperiod. In this manner, 28.asf can be executed every rotation periodwithout having to skip data acquisition cycles.

Harmonics of an incomplete rotational period in conjunction with apassive period may also be useful in applications where one or moreoptical elements are re-positioned every rotational period of modulator22 to select amongst two or more distinct optical paths. For example,analyzer 100 is configured to measure the spatial components of anextended source and a spectrometer is inserted before detector 26 toisolate a specific spectral component of the spatially-encoded signal.The spectrometer grating is stepped once per rotation period to the nextwavelength during the passive period. Preferably, the passive period islong enough such that any residual motion of the optical element(s) isdamped to an acceptable level prior to re-starting the DAQ. In thismanner, the spectral properties of each spatial component can be mappedout over a small number of rotation periods. Another example is whereanalyzer 100 is configured to measure the spectral components of anextended source and a mirror or other optical element is mounted on amovable stage to isolate specific portions of the extended source alongone or more spatial axis. The movable stage is stepped once per rotationperiod during the passive period. In this manner, the spatial andspectral properties of an extended source can be mapped out over a smallnumber of rotation periods. Another example is where analyzer 100 isconfigured to measure the spatial components of a two-dimensionalextended source along a first spatial axis and a mirror or other opticalelement is mounted on a movable stage to isolate specific cross sectionsof the extended source along a second spatial axis. The movable stage isstepped once per rotation period to the isolate the next specific crosssection of the extended source during the passive period. In thismanner, a two-dimensional image of the extended source can be obtainedover a small number of rotation periods.

In another embodiment of analyzer 100, harmonics of two or moreincomplete rotation periods may be combined to increase the number ofencoding channels without increasing the number of harmonics in theencoded beam. In this manner, the total modulation bandwidth of theencoded beam, and thereby the bandwidth of the signal generated bydetector 26, can be minimized. FIG. 11B illustrates two methods toincrease the spatial resolution of the encoding of target image 52.Modulator 22G comprises two set of radiation filters which are harmonicsof incomplete rotational periods. Radiation filters 50.34 and 50.35 areharmonics of the first half of the rotation period, and radiationfilters 50.34′ and 50.35′ are harmonics of the second half of therotation period. Radiation filters 50.34 and 50.34′ (50.35 and 50.35′)have the same phase and frequency. In addition, radiation filters 50.34and 50.34′ (50).35 and 50.35′) have the same radial width. As seen inFIG. 11B, radiation filter 50.34′ is displaced along the radial axiswith respect to radiation filter 50.34 by a distance greater than orequal to the radial width, and radiation filter 50.35′ is displacedalong the radial axis with respect to radiation filter 50.35 by adistance less than the radial width. As such, the total number ofdistinct encoding channels is four and the total number of distinctencoding frequencies and phases is two. To use modulator 22G, thesub-signal separator 28.sss of radiation analyzer 100 would separate theencoded signal into two sub-signals, 27.1 and 27.2, corresponding to thefirst half and the second half of the rotation period of modulator 22G,respectively. 27.1 would be processed by decoding algorithm 28.dec toyield the amplitudes of the components encoded by 50.34 and 50.35, and27.2 would be processed by decoding algorithm 28.dec to yield theamplitudes of the components encoded by 50.34′ and 50.35′. In thismanner, four radial sections of target image 52 can be determined usingtwo encoding functions.

In the preceding discussion, the number of incomplete rotation periodsand passive periods, the number of filters in each incomplete rotationperiod, and the configuration of annular segments comprising theincomplete rotation periods (e.g., the radial positions, radial widthsand angles subtended) were chosen for clarity and are not meant to limitthe scope of the invention.

Hyper-Spectral Imaging Analyzer

In some applications, it is necessary to measure a number of spectralcomponents of a limited collection of discrete radiation emittingsamples. Examples of collections of radiation emitting samples includemulti-dye, multi-capillary (or multi-lane) electrophoresis, multi-dye,multi-sample fluorescent assay, and a linear array of optical fiberscontaining spectral components from a remote sampling location.Typically, a CCD camera in conjunction with optics that project spatialinformation along a first axis and spectral information along a secondaxis are used for this purpose. Significant advantages in cost andperformance can be realized if the CCD camera is replaced by a singlephoto-multiplier tube (PMT) and a multi-channel optical encoder.

Another embodiment of analyzer 100 depicted in FIG. 1, Hyper-SpectralImaging Analyzer is designed to measure a plurality of spectralcomponents individually selected from two or more radiation emittingsamples substantially simultaneously. Radiation source 24 is acollection of two or more radiation emitting samples, each said sampleemitting radiation in a plurality of selected spectral components.Radiation emitted by source 24 is imaged by pre-encoder optic 36A, aone-dimensional hyper-spectral imaging optic, to form target image 52 onmodulator 22. Target image 52 comprises a plurality of spectralcomponents (individually selected from each of the radiation emittingsamples), substantially separated from one another along a common radialaxis of modulator 22. Modulator 22 includes a number of radiationfilters to encode target image 52 to provide an encoded beam comprisingtwo or more encoded components. Preferably, target image 52 is alignedwith said radiation filters such that said encoded components have asubstantially one to one correspondence with said selected spectralcomponents. The encoded beam is collected, directed and focused withpost-encoder optic 36B onto detector 26. Computer 28 then analyzes thesignal generated by detector 26 in response to the encoded beam todetermine the amplitudes of the encoded components.

FIG. 12A and FIG. 12B are a schematic top-view and a schematicside-view, respectively, of embodiment HS of pre-encoder optic 36A,36A(HS), used to project dispersed spectral components of radiationemitting samples 24.HS.1 and 24.HS.2 along a common encoding axis,X_(e). As shown in FIG. 12A and FIG. 12B, pre-encoder optic 36A(HS)comprises two collection lenses, 36A(HS).C.1 and 36A(HS).C.2, a singlediffraction grating 36A(HS).DG, and two focusing lenses, 36A(HS).F.1 and36A(HS).F.2. Collection lenses 36A(HS).C.1 and 36A(HS).C.2 arepositioned along a substantially common collection axis, X_(c). Thecollection lenses are positioned to collimate radiation emitted from tworadiation emitting samples, 24.HS.1 and 24.HS.2, arrayed along asubstantially common sample axis, X_(s). The collimated radiation beamsare diffracted by diffraction grating 36A(HS).DG, and focused byfocusing lenses 36A(HS).F.1 and 36A(HS).F.2 (arrayed along asubstantially common focusing axis, X_(f)), to form two dispersedimages, 52.HS.1 and 52.HS.2, substantially in a common encoding plane,and with the respective dispersion axes substantially along a commonencoding axis, X_(e). Using pre-encoder optic 36A(HS), target image52.HS comprises two dispersed images, 52.HS.1 and 52.HS.2, correspondingto radiation from samples 24.HS.1 and 24.HS.2, respectively,substantially separated from one another along encoding axis X_(e), andeach having the respective dispersion axis along encoding axis X_(e).

As shown in FIG. 12B, the plane of diffraction grating 36A(HS).DG istilted and the positions of focusing lenses 36A(HS).F.1 and 36A(HS).F.2are engineered to direct zeroth-order, non-diffracted radiation out ofthe preferred beam path. As shown in FIG. 12A, pre-encoder optic 36A(HS)incorporates one or more bandpass filters 36A(HS).BPF to prevent the twodispersed images from overlapping one another. If samples 24.HS.1 and24.HS.2 are excited with excitation radiation, it is preferable thatbandpass filter 36A(HS).BPF has finite transmission at the wavelength(s)of the excitation radiation such that the sub-image of the excitationradiation can be used for alignment purposes. In the present invention,pre-encoder optic 36A(HS) is to be used with modulator 22HS shown belowin FIG. 12C; i.e., encoding axis X_(e) is in the plane and along aradial axis, R, of modulator 22HS. However, pre-encoder optic 36A(HS)can also be used with a linear detector array, a scanning aperture, oran addressable spatial light modulator. These and other variants andapplications of pre-encoder optic 36A(HS) are within the scope of theinvention.

FIG. 12C is a schematic of embodiment 22HS of modulator 22 to be used inHyper-Spectral Imaging Analyzer with pre-encoder optic 36A(HS).Modulator 22HS includes two groups of radiation filters, 59.HS.1 and59.HS.2, for encoding the dispersed images of the two radiation emittingsamples, 24.HS.1 and 24.HS.2, respectively. Each sub-pattern includes anumber of radiation filters for measuring selected spectral componentsfrom each sample. In addition, each sub-pattern includes a complementaryfilter pair positioned at the expected radial position for an alignmentspectral component (expected in each radiation emitting sample) forcalibration and alignment purposes. Examples of alignment componentsinclude scattered excitation energy, Raman lines, and spectral featuresin one or more optical elements. Preferably, the signals from the twofilter pairs are used as input for the Alignment Calibration Algorithm28.utl(ACA), which in turn, generates one or more control signals toposition one or more optical elements to align target image 52 ontomodulator 22HS.

In Hyper-Spectral Imaging Analyzer there are two obvious competingencoding strategies: 1) separating the sub-images to obtain highersignal levels at the expense of spectral resolution, or 2) interlacingthe sub-images to obtain higher spectral resolution at the expense ofsignal level. If higher spectral resolution is needed, a multi-band-passfilter can be inserted between source 24.HS (comprising 24.HS.1 and24.HS.2) and detector 26, thereby allowing the dispersed sub-images tobe interlaced with a substantial increase in spectral resolution.However, this increased spectral resolution comes at the expense ofsignal level which is reduced by the multi-band-pass filter.

In FIG. 12A, FIG. 12B and FIG. 12C, the optical geometry and the numberof radiation emitting samples, optical components, and the number andconfiguration of radiation filters (and filter pairs) was chosen forclarity, it being understood that arbitrary numbers of radiationemitting samples, optical components, radiation filters, andcomplementary filter pairs are within the scope of the invention.

Interlaced Excitation Encoder

In some applications, it may be desirable to measure a samples responseto two or more different components of excitation radiation. Examples ofexcitation radiation sources include a collection of different lasers, amulti-line laser or low-pressure gas lamp combined with a diffractive orrefractive optic to separate the emission lines, optical fibers, orlamp/filter combinations. Examples of samples include amulti-lane/multi-capillary electrophoresis, and a collection of distinctfluorescence emitting (or Raman scattering) samples arranged in a lineararray. Such and other examples of excitation components and samples arewithin the scope of the invention. In some instances, it may also bedesirable to measure a samples response to two or more differentexcitation components substantially simultaneously. For example, somesamples are altered by the excitation radiation such that the results ofa sequence of excitation/response measurements may differ depending uponthe order of the applied excitation components. Another example is asample which is flowing in a process stream (e.g., electrophoresis orcell flow cytometry) where the dwell time at the location of themeasurement is insufficient to make the excitation measurements inseries. The interlaced excitation encoder described below (providesgroups of encoded excitation beams, comprising radiation from two ormore excitation sources to a collection of samples) permits the emitted,scattered, transmitted or reflected radiation from a sample in responseto two or more different excitation components to be detectedsubstantially simultaneously.

Interlaced Excitation Encoder provides two or more excitation groups,comprising two or more encoded excitation beams, to two or more samplesin a collection. Interlaced Excitation Encoder comprises the majority ofthe components of analyzer 100 and an Excitation Interlacing Optic.Excitation Interlacing Optic comprises a pre-encoder component and apost-encoder component. The pre-encoder component of ExcitationInterlacing Optic uses one or more diffractive, refractive or reflectiveelements (or various combinations thereof) to produce (an array ofsub-images from each radiation source) multiple sub-images of two ormore radiation sources (e.g., laser lines, individual lasers, diodes,lamp/filter combinations), such that the sub-image arrays of said two ormore radiation sources are interlaced along an encoding axis in anencoding plane (e.g., RGB-RGB-RGB-RGB, where R, G and B correspond tosub-images from a long, medium and short wavelength laser,respectively). A multi-channel encoder (e.g., analyzer/encoder 100)encodes each sub-image with a substantially unique modulation functionto produce an encoded interlaced excitation beam comprising groups ofencoded excitation components, wherein said groups comprises encodedcomponents from each of said radiation sources (e.g., RGB comprises onegroup). Alternatively, one could also place the interlacing optic afterthe encoder. In this case one would encode RRRR-GGGG-BBBB and theinterlacing optics would construct the excitation groups (RGB) out ofthe encoded beams. The post-encoder component of Excitation InterlacingOptic (e.g., a collection of objective lenses, wherein the number in thecollection is substantially equal to the number of samples) focuses eachsaid group onto a corresponding sample in a collection of samples.Preferably, the sub-images of the encoded beams comprising a given groupare focused on a common spot on the corresponding sample. Preferably,the intensities of the sub-images are encoded without varying thefocused spot size on the sample. More preferably, the intensities of thesub-images are encoded with a substantially uniform spatial illuminationalong one or more axes on the sample.

In response to the encoded excitation radiation, the samples in thecollection emit, scatter, transmit or reflect response radiation. Inmost instances (e.g., in the linear approximation), the responseradiation is encoded with an intensity modulation function that issubstantially identical to that of the corresponding encoded excitationbeam. In response to the excitation radiation, each said sample emits orscatters one or more response components (or beams) of radiation.Preferably, the array of groups of encoded excitation beams are alignedwith the collection of samples such that a substantially one-to-onecorrespondence exists between a given encoded response component and agiven sample/excitation combination (i.e., each sample emits or scattersone encoded response beam for each excitation source. Excitationcross-talk, resulting from an encoded excitation beam exciting more thanone sample, is to be avoided. This could be accomplished by placingradiation-blocking obstructions between the samples in the collection.).The encoded response beams are collected, directed, and focused bypost-encoded optic 36B onto detector 26, and the signals generated bythe detector in response to the encoded response beams are analyzed bycomputer 28 to determine the amplitudes of the encoded components.

If called for by the application, the spectral properties of the encodedresponse components are measured by inserting a spectrometer or otherwavelength filtering device between post-encoder optic 36B and thedetector and scanning the wavelength of the radiation transmitted to thedetector. More preferably, a spectrograph or other wavelength separatingdevice is used to direct a number of selected spectral components of theencoded beam to an equal number of detectors. Most preferably, computer28 would include a sufficient number of analog-to-digital converters(ADCs) such that the signals generated by the detectors in response tothe encoded beam could be analyzed substantially simultaneously. In thismanner, the spectral properties of the response of a collection ofsamples to one or more sources of excitation radiation can be measuredsubstantially simultaneously.

Secondary Encoder Timing Signal Synchronization

It may be advantageous to replace the timing and reset signals generatedby optical switches 70 and 71 in multi-purpose radiation analyzer 100with a commercially available Incremental Rotary Encoder (IRE). The IREis a robust, well-established technology which provides both anincremental signal (event, interrupt) and a reset signal (event,interrupt) in response to rotation. The IRE would be mounted on spindlemotor 42 and would be interfaced to computer 28 by providing theincremental signal and the reset signal of the IRE to a trigger mappingalgorithm, 28.tma, which would output a software generated trigger eventto 28.adc, and a decoding algorithm reset event to 28.dec. Onecomplexity in such an approach is compensating for the relative angularoffset between the reset signal of the IRE and the zero angle positionof modulator 22; i.e., the relative position of zero degrees as definedby the pattern of modulator 22 and the reset position on the IRE. Onesolution to this problem is to use a one-bit function generator clockedby the IRE incremental signal (provides time base) and triggered by theIRE reset signal (defines the start of the generated function). Theoutput of the one-bit function generator provides the trigger signal for28.adc and the reset signal for 28.dec. The pattern of the one-bitfunction generator is determined by analyzing the waveform obtained bysampling the signal generated by detector 26 using the incrementaloutput from the IRE as the trigger for 28.adc and the reset signal fromthe IRE to define the start and end of the data acquisition interval.The waveform (i.e., the output from detector 26 over a complete periodof the rotation of modulator 22 sampled at the IRE interval) is analyzedby curve fitting to an expected waveform (e.g., the theoretical outputof detector 26 over a complete period of the rotation of modulator 22sampled at the IRE interval with zero phase shift between the IRE resetsignal and the pattern on modulator 22) to determine the relativephase(s) between the IRE reset and the sub-pattern(s) on modulatorpattern 22. During this synchronization procedure, the radiation sourcecan be a reference lamp combined with an intensity mask to isolate oneor more known encoded components. More preferably, the synchronizationprocedure would use a dedicated radiation source, a dedicated detectorand one or more dedicated reference filters on modulator 22 to provide awell-known reference waveform for the analysis. (e.g., the system usedto illuminate and/or isolate specific radiation filters described abovein the FIRST-ORDER AMPLITUDE CORRECTION can be used to provide a knowndetector signal for analysis.) Once the relative phase between the IREand modulator 22 is determined, a mathematical relationship between thetrigger and reset signals from the IRE and the appropriate trigger andreset signals (events) to 28.adc and 28.dec, respectively, can beestablished. Preferably, the trigger signals to 28.adc are integermultiples or rational fractions (e.g., 4, 3, 2, 1, ½, ⅓, ¼) of the IREincremental signals, and the trigonometric look-up table used by 28.decis constructed with a global phase factor to account for any residualphase shift (e.g., that caused by the coarseness of the incrementalsignal IRE, and/or any latency between the incremental signal and thesoftware-generated trigger event) between the software-generated ADCtrigger signals and the pattern on modulator 22.

The output of the synchronization procedure would be a lookup tablewhich defines the one-bit function generator. The one-bit functiongenerator may contain one or more passive periods, or multiple,independent (e.g., multiple function generators having a common timebase) outputs to synchronize the data acquisition to modulator patternswhich include harmonics of incomplete rotational periods or applicationswhich involve sampling multiple detectors.

Multivariate Chemometric Analyzer

Due to the ability to configure the radial position and radial width ofradiation filters and filter pairs on modulator 22 for specificapplications, the present invention is ideal for use as a multivariateChemometric analyzer. Another embodiment of analyzer 100 depicted inFIG. 1A, Multivariate Chemometric Analyzer is designed to measure theconcentrations of selected analytes in a sample substantiallysimultaneously. In general, analytes absorb, and/or scatter, and/or emitradiation as a function of their respective concentrations. In thediscussion that follows, we consider an instrument designed to measure afirst plurality of selected analytes that absorb radiation as a functionof their respective concentrations It is understood that otherembodiments of analyzer 100 designed to measure two or more analytesthat scatter or emit radiation are within the scope of the invention.

Radiation source 24 provides broadband radiation encompassing at leastone spectral feature from each of the selected analytes. Pre-encoderoptic 36A includes at least one diffractive, refractive or filteringelement to form a dispersed image 52 along a radial axis of modulator22. Modulator 22 includes a second plurality of radiation filters and/orradiation filter pairs to encode a third plurality of selected spectralcomponents of radiation from the source 24 to provide an encoded beam asmodulator 22 is rotated about axis 40. Each filter occupies an annularregion (or annular segment) having a radial position substantiallydefining the center wavelength of a corresponding spectral component,and a radial width substantially defining the bandwidth of acorresponding spectral component.

Post-encoder optic 36B collects and directs the encoded beam onto atleast one radiation detector 26, which provides encoded signal 27 tocomputer 28.adc. Computer 28 includes a decoding algorithm 28.dec, whichdecodes signal 27 to provide the amplitudes of one or more of theencoded spectral components as inputs for application-specific function28.asf, a Chemometric algorithm, computes the concentrations of one ormore of the selected analytes.

Preferably, one or more samples or sample cells (e.g., sample 38 of FIG.1A) are placed between source 24 and detector 26 for multivariateChemometric analysis.

Preferably, the performance of the Chemometric algorithm can beoptimized by the judicious selection of the spectral components. Forexample, the radial position and radial width of the radiation filtersand/or radiation filter pairs on modulator 22 can be engineered toprovide optimized spectral components that minimize the resultingconcentration error computed by 28.asf from an intensity (measurement)error in one or more spectral components. In this manner, the encodedcomponents resulting from the rotation of modulator 22 about rotationaxis 40 provide an ideal input to the Chemometric algorithm. For a givendispersed target image 52, there are unique modulator patterns thatprovide ideal spectral input for a specific multivariate Chemometricapplication. In this manner, modulator pattern 21 of MultivariateChemometric Analyzer corresponds to a specific target image 52 and aspecific set of analytes. One method to optimize modulator 22 forChemometric applications is described below.

Preferably, radiation source 24 includes at least one reference spectralcomponent, where the intensity is substantially unaffected by theconcentrations of the analytes, and modulator 22 includes acorresponding radiation filter to provide an encoded referencecomponent, which is used to normalize the amplitudes the spectralcomponents used in the Chemometric algorithm. More preferably,Multivariate Chemometric Analyzer employs two or more reference spectralcomponents and two or more corresponding radiation filters (or filterpairs) to provide encoded reference components used by 28.asf to gaugevariations in the spectral output of source 24 (e.g., the temp of asubstantially blackbody radiator) and/or the spectral responsivity ofdetector 26. In this manner, Chemometric algorithm 28.asf candistinguish between changes in the concentrations of the analytes, andchanges in the output of source 24 or changes in the responsivity ofdetector 26.

Preferably, a sample (e.g., sample 38 of FIG. 1A) is inserted in theoptical path between source 24 and detector 26 to provide a controlledoptical path of known length. More preferably, sample 38 is part of asampling system that includes a pump and computer-controlled valves suchthat one or more cells can be alternately filled with a zero gas; i.e.,a gas containing zero concentrations of the Chemometric analytes, andthe sample gas, which may contain the analytes. Examples of zero gasinclude air, nitrogen argon, etc. In this manner, the amplitude of oneor more spectral components filtered by the sample gas can be referencedto (or normalized by) the amplitude of one or more spectral componentsfiltered by the zero gas.

In one embodiment of Multivariate Chemometric Analyzer, a cellcontaining sample 38 and detector 26 are combined into a single unit(e.g., a luft detector).

Preferably, Multivariate Chemometric Analyzer includes one or morespectral calibration filter groups (described below inSpectral-Calibration Analyzer) to gauge the alignment of target image 52onto the radial axis of modulator 22.

Preferably, Multivariate Chemometric Analyzer includes one or moredetector responsivity frequency calibration filter groups (describedbelow in Detection-System Frequency-Dependence Compensation Analyzer) tonormalize various encoded components for the frequency dependence ofdetector 26.

Configuration Method for Multivariate Chemometric Analyzer

In this section we describe a method (e.g., a software algorithm) forgenerating an optimized pattern, 21, for spatial radiation modulator 22of Multivariate Chemometric Analyzer to analyze (e.g., identificationand quantification) a group of analytes in one or more samples.

FIG. 13A is a schematic representation of one method to configurationmodulator 22 for an embodiment of Multivariate Chemometric Analyzer thatmeasures the concentration of two analytes, Ψ₁ and Ψ₂, which absorbradiation as a function of their respective concentrations, ξ₁ and ξ₂,it being understood that the method can be generalized to otherembodiments of analyzer 100 designed to measure two or more analytesthat scatter or emit radiation. Such and other variations are within thescope of the invention. As shown by the vertical dashed line in FIG.13A, the method inputs corresponding spectra for each analyte, ψ₁(λ) andψ₂(λ), each having at least one concentration-dependent spectral featurein at least one of the spectral ranges of source 24, of knownconcentration and experimental conditions. Examples of experimentalconditions include optical path length, temperature, humidity andpressure. Preferably the spectra are in an electronic format.

As shown by the horizontal dashed line in FIG. 13A, the method inputsparameters that define a set of two initial spectral windows, T_(MC.1)⁽⁰⁾(λ) and T_(MC.2) ⁽⁰⁾(λ), which are defined by center wavelengths, λ₀^(MC.1) and λ₀ ^(MC.2), and bandwidths, Δλ_(MC.1) and Δλ_(MC.2),respectfully. Although more elaborate models, (e.g., which account forfinite spectral resolution), are also within the scope of the invention,in the discussion that follows, we consider the following model forT_(MC.1) ⁽⁰⁾(λ) and T_(MC.2) ⁽⁰⁾(λ):

$\begin{matrix}{{T_{j}(\lambda)} = \begin{Bmatrix}0 & {\lambda < \left( {\lambda_{0}^{j} - \frac{\Delta\;\lambda_{j}}{2}} \right)} \\1 & {\left( {\lambda_{0}^{j} - \frac{\Delta\;\lambda_{j}}{2}} \right) \leq \lambda \leq \left( {\lambda_{0}^{j} + \frac{\Delta\;\lambda_{j}}{2}} \right)} \\0 & {\lambda > \left( {\lambda_{0}^{j} + \frac{\Delta\;\lambda_{j}}{2}} \right)}\end{Bmatrix}} & (12)\end{matrix}$Preferably, the parameters defining the initial spectral windows, {λ₀^(MC.1), Δλ_(MC.1)}⁽⁰⁾ and {λ₀ ^(MC.2), Δλ_(MC.2)}⁽⁰⁾, are stored in oneor more text files to be imported at the start of an optimizationsession, updated by the optimization procedure, and exported to anoptimized spectral window file at the end of the optimization process.In this manner, the optimized spectral windows can be used as initialspectral windows for subsequent optimizations.

As shown in FIG. 13A, algorithm 80 calculates the normalized spectralcomponent intensities S_(MC.1) and S_(MC.2) as a function of the analyteconcentrations

$\begin{matrix}{S_{j} = {\frac{1}{S_{j}^{0}}{\int{{\mathbb{d}\lambda}\;{I(\lambda)}{T_{j}(\lambda)}{\prod\limits_{k = 1}^{2}{\psi_{k}\left( {\lambda;\xi_{k}} \right)}}}}}} & (13)\end{matrix}$where I(λ) is the wavelength-dependent intensity of radiation emitted bysource 24 that reaches detector 26 when modulator 22 is replaced with auniformly reflective (or uniformly transmissive) substrate 23,j={MC.1,MC.2}, and S_(MC.1) ⁰ and S_(MC.2) ⁰ are the intensities ofspectral windows in the zero concentration limit (e.g., the sample cellfilled with zero gas or zero liquid)S _(j) ⁰ =∫dλI(λ)T _(j)(λ)  (14)The normalized intensity of the j={MC.1, MC.2} spectral component due tothe absorbance of the k={Ψ₁, Ψ₂} analyte is defined asS _(jk) =e ^(−ℑ) ^(jk) ^((ξ) ^(k) ⁾  (15)where, the absorbance functions (which include the effects path length,pressure, temperature etc . . . ), ℑ_(jk), are expanded in a polynomialin the k-th analyte concentrationℑ_(jk) =A _(jk) ξ _(k) +B _(jk)ξ_(k) ² +C _(jk)ξ_(k) ³+  (16)

In the linear absorbance limit (i.e., the low concentration limit), theS_(jk) can be approximated asS _(jk) ≈e ^(−A) ^(jk) ^(ξ) ^(k) ,  (17)and, the system of Chemometric equations becomes−ln(S)≈Aξ,  (18)which can be inverted to recovered the analyte concentrations as afunction of the normalized spectral componentsξ≈A ⁻¹[−ln(S)],  (19)where, A⁻¹ is the inverse Chemometric coefficient matrix.

As shown in FIG. 13A, algorithm 81 inputs the normalized spectralcomponents for different analyte concentrations and outputs the inverseChemometric coefficient matrix, A⁻¹. Using A⁻¹ and one or more intensityerrors δS={δS_(MC.1),δS_(MC.1)} as input, algorithm 82 calculates atleast one concentration error of each analyte as a function of theintensity errors of each spectral component. Preferably, algorithm 82calculates a statistical sample of concentration errors resulting from asubstantially random distribution of intensity errors. Alternatives tothe statistical approach include evaluating one or more conditionnumbers of the inverse Chemometric coefficient matrix, A⁻¹. In thiscase, A⁻¹ can be used as input to algorithm 83 bypassing 82 altogether.Such and other gauges of noise transfer are within the scope of theinvention.

In the linear absorbance limit, the concentration errors δξ are given byδξ≡A ⁻¹[ln(1+δS)]  (20)where, δξ={δξ₁,δξ₂} are the concentration errors (i.e., the falseconcentrations) of Ψ₁ and Ψ₂ in response to the intensity errorsδS={δS_(MC.1),δS_(MC.1)}.

As shown in FIG. 13A, algorithm 83 inputs one or more concentrationerrors and outputs at least one current noise merit function χ^((n)).Examples of noise merit function include various condition numbers ofA⁻¹. In FIG. 13A, we consider a noise merit function is based on astatistical analysis (e.g., root-mean-square) of the concentration errorobtained from random intensity error on the spectral windowsM.F.=√{square root over ((δξ₁)²+(δξ₂)²)}{square root over((δξ₁)²+(δξ₂)²)},  (21)where, (δξ₁) and (δξ₂) are the corresponding statistical meanconcentration errors of Ψ₁ and Ψ₂ calculated by 28.asf in response to arandom intensity noise; i.e., a random distribution of intensity errorsδS_(MC.1) and δS_(MC.2).

As shown by the dashed circle in FIG. 13A, algorithm 84 compares currentmerit function χ^((n)) to the previous best merit function, χ^(opt). Ifcurrent merit function χ^((n)) is better than previous best meritfunction χ^(opt), χ^(opt) is replaced by χ^((n)), and T_(MC.1) ^(opt)and T_(MC.2) ^(opt) are replaced by T_(MC.1) ^((n)) and T_(MC.2) ^((n)).On the first iteration of the Optimization Loop shown in FIG. 13A,χ^(opt), and {T_(MC.1) ^(opt), T_(MC.2) ^(opt)}, are initialized withχ⁽⁰⁾, and {T_(MC.1) ⁽⁰⁾, T_(MC.2) ⁽⁰⁾}, respectively.

As shown in FIG. 13A, the Optimization Loop defined by the followingalgorithm sequence: 85, 80, 81, 82, 83, 84, and back to 85, repeats asalgorithm 85 generates subsequent sets of spectral windows, T_(MC.1)^((n+1)) and T_(MC.2) ^((n+1)), obtained by systematically varying thecenter wavelength and bandwidth of the initial spectral windows e.g., bysearching the entire parameter space of center wavelengths andbandwidths provided by target image 52.

Once an optimum set of spectral windows has been identified, thecorresponding center wavelengths and bandwidths must be mapped onto theradial axis of modulator 22. As shown in FIG. 13A, algorithm 86 inputsat least one dispersion function λ₅₂(r) (preferably in electronicformat) to relate spectral properties of target image 52 to the radialposition of modulator 22. Dispersion function λ₅₂(r) relates thewavelength of dispersed image 52 as a function of radial position onmodulator 22. The dispersion function is inverted to yield r₅₂(λ) theradial position on modulator 22 as a function of wavelength. The inversedispersion function, r₅₂(λ), is used by algorithm 86 to translate theset of optimized center wavelengths and bandwidths into a correspondingoptimized set of annular regions (or annular segments; e.g., as shown inFIG. 11A), R_(MC.1) ^(opt) and R_(MC.2) ^(opt), on modulator 22. In thismanner optimized annular regions (or annular segments) R_(MC.1) ^(opt)and R_(MC.2) ^(opt) have a substantially one-to-one correspondence tooptimized spectral windows T_(MC.1) ^(opt) and T_(MC.2) ^(opt),respectively.

Once the optimized annular regions (or annular segments) R_(MC.1) ^(opt)and R_(MC.2) ^(opt) have been identified, algorithm 87 patternsradiation filters 50.MC.1 and 50.MC.2 (or filter pairs) comprising aplurality of sub-regions (having optical characteristics substantiallydifferent from substrate 23) within each said corresponding annularregion (or annular segment) to provide a corresponding set a uniquemodulation function, to encode the optimized spectral components.Preferably, the sub-regions are patterned to provide modulationfunctions that are substantially orthogonal smooth functions ordigitized replicas of orthogonal smooth functions having three or moredistinct levels of contrast as the spatial radiation modulator isrotated about rotation axis 40. More preferably, the modulationfunctions are of the form sin²(mθ+pπ/4). Most preferably, the harmonics,m, are selected to be prime numbers to minimize cross-talk (i.e.,maximize the inter-channel orthogonality) between the encoded optimizedspectral components. In this manner the optimized spectral componentsencoded as modulator 22 rotates about rotation axis 40 correspond tooptimized spectral windows T_(MC.1) ^(opt) and T_(MC.2) ^(opt).

Preferably, optimized pattern 21 is output in an electronic formatcompatible with a variety of printing and lithographic patterngenerators (e.g., the design exchange format, or DXF).

Note that optimized spectral windows T_(MC.1) ^(opt) and T_(MC.2) ^(opt)are mapped onto annular regions of modulator 22, which encompassradiation filters and/or filter pairs that encode selected spectralcomponents of target image 52. In other words, the spectral componentsare defined by the overlap of target image 52 and the annular regions ofthe radiation filters and/or filter pairs, which are engineered fromoptimized spectral windows T_(MC.1) ^(opt) and T_(MC.2) ^(opt). In thismanner, the optimized Chemometric encoder pattern 21 on modulator 22 ofthe present invention corresponds to a solution of the Chemometricoptimization problem, and replaces the custom bandpass filter sets usedin traditional non-dispersive chemical and fluorescence analyzers.

Hydrocarbon Example of Multivariate Chemometric Analyzer

FIG. 13B and FIG. 13C illustrate a practical example of theaforementioned process, demonstrating the correspondence between theanalyte spectra, the optimized spectral windows, and the radiationfilters on modulator 22HC for the Chemometric analysis of fivehydrocarbons.

FIG. 13C shows the respective transmission spectra of the hydrocarbonsmethane, propane, butane, pentane and hexane, in the 3.0 to 3.6 micronspectral range, and the optimized spectral windows T_(HC.1) throughT_(HC.5). Optimized spectral windows T_(HC.1) through T_(HC.5) wereobtained using the method described above. FIG. 13C also includes areference spectral window T_(HC.R), located outside the spectral rangewhere the analytes absorb radiation to provide a measure of the overallintensity of source 24 and/or the responsivity of detector 26.Preferably, Multivariate Chemometric Analyzer employs two or morereference spectral components to gauge variations in the spectral outputof source 24 and/or the spectral responsivity of detector 26.

FIG. 13B shows the optimized configuration of radiation filters 50.HC.1through 50.HC.5, and 50.HC.R, on modulator 22HC. The dashed linesbetween FIG. 13C and target image 52.HC are used to illustrate theone-to-one correspondence between the Chemometric-optimized spectralwindows and the engineered pattern of radiation filters on modulator22HC.

In the description of Multivariate Chemometric Analyzer and thecorresponding configuration method, the position of sample 38 was chosenfor illustrative purposes and is not intended to limit the scope of theinvention.

In the description of Multivariate Chemometric Analyzer and thecorresponding configuration method, the number of analytes was chosenfor illustrative purposes and is not intended to limit the scope of theinvention.

In the description of Multivariate Chemometric Analyzer and thecorresponding configuration method, the number of reference componentswas chosen for illustrative purposes and is not intended to limit thescope of the invention.

In the description of Multivariate Chemometric Analyzer and thecorresponding configuration method, one or more radiation filters can bereplaced with complementary or collective radiation filter pairs. Suchand other variations are within the scope of the invention.

In the description of Multivariate Chemometric Analyzer and thecorresponding configuration method, the number of target images andnumber of radiation detectors was chosen for illustrative purposes andis not intended to limit the scope of the invention. In some Chemometricapplications, it may be advantageous to include two or more spectralranges (target images), bandpass and/or dichroic mirrors, and two ormore radiation detectors.

By changing the spectral range(s) of the dispersed images(s) 52, anddesigning a suitable pattern for modulator 22, the instrument andprocess described above for the hydrocarbons methane, propane, butane,pentane and hexane, is applicable to a wide variety of chemical speciesin the gas, liquid and solid phases. For example, volatile organicchemicals, solvents, water, pollutants, gasoline additives, anestheticagents, chlorofluorocarbons (CFCs), flora, the constituents of naturalgas, and chemical weapons all have chemical signatures, which can beused to quantify and discriminate. Applications to these and otherchemical signatures are within the scope of the invention. Theinstrument and process described above for the hydrocarbons methane,propane, butane, pentane and hexane is also applicable to thediscrimination and quantification of fluorescent dyes. Applications tothe identification and quantification of chemical compositions based onother radiation-based spectral signatures (e.g., fluorescence, Ramanlines, atomic emissions) are within the scope of the invention.

Preferably, a class of instruments sharing a substantially commonplatform (e.g., sharing substantially identical pre-encoder optic 36A,post-encoded optic 36B, sample cell 38, detector 26 and computer 28),can be derived from Multivariate Chemometric Analyzer, where modulatorpattern 21 is designed for a specific application (i.e., the modulatorpattern 21 and 28.asf are the principal differences between specificinstruments in the class). In this manner, the economics of scale can beapplied to the manufacturing process for a diverse line ofapplication-specific Chemometric analyzers.

Spectral-Calibration Analyzer

One of the unique aspects of the present invention is the ability toconstruct complementary filter pairs that create a single encodedcomponent where the magnitude and phase are determined by the relativeproportion of radiation incident on the two filters comprising the pair.In another embodiment of radiation spectrum analyzer 100,Spectral-Calibration Analyzer, the radial position and radial width ofpairs of complementary filters are chosen to probe the relative positionof specific, known spectral features in target image 52 for the purposeof gauging the alignment of target image 52 onto the radial axis ofmodulator 22. In this manner, the magnitude and phase of the componentencoded by the complementary pair 55 can be used to gauge the alignmentof target image 52 on modulator 22.

Examples of known spectral features suitable to be used for spectralcalibration include various absorption features of H₂O, CO₂, methane,plastics and other common chemicals, the emission spectra of commondyes, excitation laser lines, diffraction patterns (e.g., interferencefringes), various Raman lines (e.g., N₂, O₂ and H₂O), and the spectraledges of common optical materials (e.g., glass, sapphire, ZnSe, Si, Ge,BaF₂, etc . . . ) and thin-film filters. These and other spectralfeatures suitable for use in gauging the alignment of target image 52onto the radial axis of modulator 22 are within the scope of theinvention.

In the following discussion, we consider spectral calibration usingabsorption signatures of methane (CH₄) and CO₂ for illustrativepurposes, and is not intended to limit the scope of the invention.

For the discussion that follows, it is convenient to define a detunedcomplementary pair radiation component:

$\begin{matrix}{{{S_{-}(\Delta)} = {\int{{\mathbb{d}\lambda}\left\{ {\frac{T_{1}\left( {\lambda + \Delta} \right)}{\Delta\;\lambda_{1}} - \frac{T_{2}\left( {\lambda + \Delta} \right)}{\Delta\;\lambda_{2}}} \right\}{\psi_{cal}(\lambda)}}}},} & (22)\end{matrix}$

and a detuned collective pair radiation component:

$\begin{matrix}{{S_{+}(\Delta)} = {\int{{\mathbb{d}\lambda}\left\{ {\frac{T_{1}\left( {\lambda + \Delta} \right)}{\Delta\;\lambda_{1}} - \frac{T_{2}\left( {\lambda + \Delta} \right)}{\Delta\;\lambda_{2}}} \right\}{\psi_{cal}(\lambda)}}}} & (23)\end{matrix}$

where, Δ is the vector displacement of target image 52 with respect tomodulator pattern 21 along the radial axis, ψ_(cal)(λ) is thewavelength-dependent transmission spectrum of the calibration analyte,and T₁(λ) and T₂(λ) are the normalized transmissions of the first andsecond filters comprising the pair, respectively

$\begin{matrix}{{T_{j}(\lambda)} = \begin{Bmatrix}0 & {\lambda < \left( {\lambda_{0}^{j} - \frac{\Delta\;\lambda_{j}}{2}} \right)} \\1 & {\left( {\lambda_{0}^{j} - \frac{\Delta\;\lambda_{j}}{2}} \right) \leq \lambda \leq \left( {\lambda_{0}^{j} + \frac{\Delta\;\lambda_{j}}{2}} \right)} \\0 & {\lambda > \left( {\lambda_{0}^{j} + \frac{\Delta\;\lambda_{j}}{2}} \right)}\end{Bmatrix}} & (24)\end{matrix}$

Preferably, the complementary filter pair corresponding to S⁻(Δ) isengineered such that the amplitude of S⁻(Δ) is nulled (i.e., goes tozero) when target image 52 is properly aligned onto the radial axis ofmodulator 22

$\begin{matrix}{{\frac{\lim}{\Delta->0}{S_{-}(\Delta)}} = 0} & (25)\end{matrix}$

Preferably, the complementary filter pair corresponding to S⁻(Δ) isengineered such that the amplitude and phase of S⁻(Δ) is single-valuedover the anticipated detuning range of target image 52 along the radialaxis of modulator 22. More preferably, amplitude of the correspondingencoded component is a strong function of the detuning of target image52 along the radial axis of modulator 22 to enable the most accurategauge of the alignment of 52 on 22.

One method for obtaining a complementary pair optimized for spectralcalibration systematically varies the respective center wavelengths andbandwidths of T₁ and T₂ to identify the parameters that minimize themerit function

$\begin{matrix}{{M.F.} = \frac{1 + {{S_{-}(0)}}}{{{S_{-}\left( \Delta_{0} \right)} - {S_{-}\left( {- \Delta_{0}} \right)}}}} & (26)\end{matrix}$

where, Δ₀ is the anticipated maximum detuning parameter. To find theoptimum complementary pair for a given calibration application, thecenter wavelength and bandwidth of the complementary filters aresystematically varied to minimize the merit function.

Once suitable parameters for T₁ and T₂ are found, a (theoretical)corresponding normalized calibration curve, F, is generated bydisplacing T₁ and T₂ relative to the calibration analyte transmissionspectrum along the radial axis of modulator 22. One such model for thenormalized calibration curve is given by

$\begin{matrix}{{F(\Delta)} = \frac{S_{-}(\Delta)}{2 - {S_{+}(\Delta)}}} & (27)\end{matrix}$

where, Δ is the wavelength detuning parameter; i.e., the vectordisplacement of target image 52 along the radial axis of modulator 22.

Preferably, the complementary filter pair corresponding to S⁻(Δ) and thecollective filter pair corresponding to S₊(Δ) are engineered such thatthe normalized calibration curve is substantially independent ofcalibration analyte concentration over a range of concentrations.

Preferably, the complementary filter pair corresponding to S⁻(Δ) and thecollective filter pair corresponding to S₊(Δ) are engineered such thattheir respective annular segments exclude annular regions or annularsegments occupied by application-specific filters; e.g., the optimizedChemometric filters are separated by radial position and/or annularsegment from the filter pairs corresponding to S⁻(Δ) and S₊(Δ).

In Spectral-Calibration Analyzer, the number and configuration of thefilter pairs in the calibration groups on modulator 22 was chosen forillustrative purposes, and is not intended to limit the scope of theinvention. In Spectral-Calibration Analyzer, the form of the meritfunction and the normalized calibration curve were chosen forillustrative purposes, and is not intended to limit the scope of theinvention.

Preferably, Spectral-Calibration Analyzer includes a translation stage(e.g., component 35 of FIG. 9B) to detune the position of target image52 along the radial axis of modulator 22 to generate an empiricalversion of Eqn. (27). More preferably, this translation stage is used inconjunction with a calibration gas of known concentration confined to asample cell of known length (e.g., similar to sample cell 38 of FIG. 1A,inserted between 24 and 26) to generate one or more calibration curvesfor subsequent use in an instrument and/or the instrument assemblyprocess. Most preferably, this translation stage is used in conjunctionwith a background analyte (e.g., CO₂, CH₄, H₂O, N₂, or O₂) to generateone or more calibration curves for subsequent use in an instrumentand/or the instrument assembly process.

Preferably, a standard calibration gas of known concentration iscontained in a sample cell of known length (e.g., sample 38 of FIG. 1A),which is located in Spectral-Calibration Analyzer's optical path betweensource 24 and detector 26, to properly normalize the calibration curves.More preferably, the complementary filter pair corresponding to S⁻(Δ) isconfined to an annular segment comprising an incomplete rotation period(as shown in FIG. 11A), and is augmented by a non-paired radiationfilter that measures substantially the same portion of target image 52.Most preferably, the complementary filter pair corresponding to S⁻(Δ) isconfined to an annular segment comprising an incomplete rotation period,and is augmented by a collective filter pair corresponding to S₊(Δ),having substantially identical radial position and radial width as thecomplementary filter pair, but occupying different annular segments;e.g., the complementary pair occupies the first half-period and thecorresponding collective filter pair occupies the second half-period ofmodulator 22 (shown below in FIG. 14C). In this manner, a normalizedcalibration curve can be obtained over a wide range of calibrationanalyte concentrations.

Preferably, the decoded amplitudes and phases from one or morecomplementary filter pairs are used to provide feedback to applicationspecific function 28.asf to compensate for the effects of imperfectalignment during operation (e.g., to compensate for changes in alignmentand modulator radius due to changes in temperature). More preferably,the decoded amplitudes and phases from one or more complementary pairsand the corresponding collective pairs (or non-paired filter) are usedto provide feedback to application specific function 28.asf tocompensate for the effects of imperfect alignment during operation;e.g., to compensate for changes in size or alignment of one or moreoptical components or fixtures in response to changes in thetemperature.

The inclusion of translation stage 35 is an added expense to analyzer100. It is therefore desirable to exclude motorized translation stage 35from mass-produced instruments. Preferably, the decoded amplitude andphase from one or more complementary pairs are used to provide feedbackfor the alignment of pre-encoder optic with respect to modulator 22during the assembly process. More preferably, the decoded amplitude andphase from one or more complementary pairs and the correspondingcollective pairs (or non-paired filter) are used to provide feedback forthe alignment of pre-encoder optic with respect to modulator 22 duringthe assembly process.

Preferably, the configuration of one or more complementary andcollective filter pairs are optimized to probe the relative alignment ofone or more spectral features of a standard calibration gas of knownconcentration (e.g., low concentrations of methane in nitrogen),contained in a sample cell of known length, in target image 52 withrespect to modulator 22. In this manner, a standard calibration gas isused as an “alignment standard” (or gauge) to provide an assemblytechnician guidance (feedback) in positioning pre-encoder optic 36A withrespect to modulator 22 during the assembly process. More preferably,the complementary and collective filter pairs corresponding to S⁻(Δ) andS₊(Δ), respectively, are optimized to probe the relative alignment ofone or more spectral features of background CO₂ and/or water vapor intarget image 52 with respect to modulator 22. In this manner, backgroundCO₂ and/or water vapor are used as an “alignment standard” (or gauge) toprovide assembly technicians with guidance (feedback) in positioningpre-encoder optic 36A with respect to modulator 22 during the assemblyprocess.

Preferably, the complementary and collective filter pairs correspondingto S⁻(Δ) and S₊(Δ), respectively, are optimized to probe the relativealignment of one or more spectral features of background CO₂ and/orwater vapor in target image 52 with respect to modulator 22 to enable anin-situ calibration process; e.g., continuously gauging the alignment oftarget image 52 with respect to modulator 22 (e.g., in response tochanges in ambient temperature), and compensating subsequent decodedcomponents and/or application-specific algorithm 28.asf for artifactsintroduced by variations in the alignment of target image 52 withrespect to modulator 22.

FIG. 14A shows the optimized calibration spectral windows T_(SC.1)through T_(SC.4), and FIG. 14B shows the resulting normalizedcalibration curves obtained for the spectral absorbance features of CH₄and CO₂ in the 3.0 to 4.5 micron region, respectively. Both calibrationcurves show single-valued behavior over a radial detuning range (i.e.,the radial displacement of target image 52 with respect to modulatorpattern 21SC of FIG. 14C shown below) of ±0.5 mm. The calibration curvefor CO₂ (dashed line) is shown to be a strong function of the detuningfactor (i.e., the translation of 52 with respect to perfect alignment on22SC) for comparable concentrations of calibration gasses, enabling thespectral calibration of analyzer 100 on ambient CO₂.

FIG. 14C shows embodiment 22SC of modulator 22, where the transmissionspectrum of CH₄ and CO₂ are used to gauge the alignment of target image52 onto the radial axis of modulator 22SC. Pattern 21SC comprises twocalibration groups, optimized to gauge the alignment of target image 52on the surface of modulator 22SC using absorption features of CH₄ andCO₂, respectively. The first calibration group, comprising complementaryfilter pair 55.SC.1 and collective filter pair, 57.SC.1, probes thetransmission spectrum of CH₄ to gauge the alignment of target image 52on modulator 22SC. The second calibration group, comprisingcomplementary filter pair 55.SC.2 and collective filter pair 57.SC.2,probes the transmission spectrum of CO₂ to gauge the alignment of targetimage 52 on modulator 22SC. As shown by the bold dot-dash line in FIG.14C, modulator pattern 21SC is divided into two half-periods.Complementary filter pair 55.SC.1 and collective filter pair 57.SC.2occupy the first half-period of modulator 22SC, and collective filterpair 57.SC.1 and complementary filter pair 55.SC.2 occupy the secondhalf-period of modulator 22SC. In this manner, the normalized detuningfactor (i.e., a point on the normalized calibration curve) can bemeasured over a period of rotation of modulator 22SC. The normalizationof the calibration curve substantially relaxes the need for acalibration gas of known quantity. Preferably, the nonnalized detuningfactor is compared with the normalized calibration curve to gauge thealignment of 52 onto 22SC.

FIG. 14D shows the optimized calibration spectral windows T_(SC.1)through T_(SC.4), and FIG. 14C shows the configuration of radiationfilter pairs (55.SC.1, 55.SC.2, 57.SC.1 and 57.SC.2) on modulator 22SCto illustrate the one-to-one correspondence between the optimizedcalibration spectral windows and the engineered pattern of radiationfilter pairs 21.

In FIG. 14C, the radiation filters comprising spectral calibrationfilter pairs 55.SC.1, 55.SC.2, 57.SC.1, and 57.SC.2 are non-adjacent.Spectral calibration filter pairs that are adjacent are useful forspectral features having a single predominant feature or well-separatedfeatures (e.g., excitation laser lines, diffraction maxima), and arewithin the scope of the invention.

The use of the 3.3 and 4.2 micron spectral absorption features of CH₄and CO₂, respectively, in the description of Spectral-CalibrationAnalyzer was chosen for illustrative purposes only. Other spectralranges, other gasses (H₂O vapor, O₂, etc . . . ) other calibrationanalytes (including liquid H₂O, absorbent dyes, fluorescent dyes), andother transmission, scattering or emission (e.g. fluorescence) spectralfeatures (e.g., the transmission cut-off of optical materials, or one ormore thin-film filters, Raman lines, and atomic emission lines) arewithin the scope of the invention.

The use of collective filter pairs 57.SC.1 and 57.SC.2 in thedescription of Spectral-Calibration Analyzer was chosen for illustrativepurposes only and is not meant to limit the scope of the invention.Other arrangements of filters and filter pairs that provide a gauge ofthe alignment of the target image with respect to the modulator patternare within the scope of the invention.

The aforementioned calibration filter pairs are equally applicable to animaging embodiment of analyzer 100, where the radial position and radialwidth of pairs of complementary filters (and/or collective filters) arechosen to coincide with specific spatial features of known position intarget image 52 (e.g., a capillary array with one or more alignmentcapillaries filled with one or more fluorescent dyes). In this manner,the magnitude and phase of the component encoded by the complementarypair can be used to gauge the alignment of target image 52 on modulator22.

Detection-System Frequency-Dependence Compensation Analyzer

One of the unique aspects of the present invention is the ability toconstruct groups of filters, with widely varying modulation frequenciesthat encode substantially identical radiation components of source 24(e.g., by substantially occupying the same annular region of modulator22, or using a dedicated calibration source). By selectively positioningthe filters in a group and judiciously selecting their respectivemodulation frequencies, one can gauge the modulation frequencydependence of detector 26 and the corresponding detection electronics.

In another embodiment of radiation analyzer 100. Detection-SystemFrequency-Dependence Compensation Analyzer, detector 26 (comprising thedetector and the associated electronics) has a responsivity (i.e.,signal output vs. modulated optical intensity input) that is a functionof modulation frequency. In addition to distorting the amplitudes, thefrequency dependence of detection system 26 imparts a relativephase-shift between encoded components that are modulated at differentfrequencies, which complicates the decoding algorithm. As a furthercomplication, the frequency dependence of detection system 26 is notstatic, but changes over time (e.g., in response to changes intemperature or average illumination). Detection-SystemFrequency-Dependence Compensation Analyzer provides an integratedmechanism to periodically calibrate the frequency dependence ofdetection system 26, and to compensate for distortions in the amplitudeand phase of the encoded components resulting from variations in thefrequency dependence of detection system 26.

FIG. 15 is a top view of radiation modulator 22FC to illustrate anotheraspect of the invention. Modulator 22FC includes three different modelcalibration filter groups 59.FC.1, 59.FC.2, and 59.FC.3, each comprisingthree filters having different modulation periods, designed to gauge thefrequency dependence of detection system 26. Calibration groups 59.FC.1,59.FC.2, and 59.FC.3 substantially measure the same radiation componentof target image 52 (e.g., by restricting the calibration filters to asubstantially common annular region) with 3 different frequencies toprovide three encoded frequency-dependence calibration components withsubstantially the same amplitude.

Computer 28.dec decodes the amplitudes and phases of the encodedfrequency-dependence calibration components. The decoded amplitudes andphases are used as input by computer frequency-dependence calibrationalgorithm 28.utl(FCA) to gauge the frequency dependence of detectionsystem 26. Computer algorithm 28.utl(FCA) outputs two calibrationcurves, amplitude vs. modulation frequency, and phase vs. modulationfrequency, which are then used by computer 28 to decode and normalizeother decoded components (not shown on modulator 22FC). Since aquadrature analysis and re-normalization of the encoded componentsexpends more than twice the computing power of decoding components withwell-know phase and normalization, it is preferred that the calibrationcurves are used to generate an updated set of decoding coefficients(which are passed by 28.utl(FCA) to 28.dec as shown in FIG. 1A):

$\begin{matrix}{{T_{m,p}^{j} \equiv {{- \left( {1 + {\delta\; a_{m}}} \right)}\frac{2}{\pi\; M}{\cos\left( {\frac{4\; j\; m\;\pi}{M} + {\left( {p + {\delta\; p_{m}}} \right)\frac{\pi}{2}}} \right)}}},} & (28)\end{matrix}$

where δa_(m), and δp_(m) are the frequency-dependent amplitude and phasecorrections, respectively, that compensate encoded component {m,p} forthe frequency dependence of detection system 26. The frequency-dependentamplitude and phase corrections δa_(m), and δp_(m), and the updateddecoding coefficients, T_(m.p) ^(j), are recalculated from thecalibration curves as often as defined by the application; e.g.,triggered by one or more temperature sensors and/or timers. In thismanner, the frequency dependence of detection system 26 is preventedfrom corrupting the results of the application-specific computeralgorithm 28.asf.

FIG. 15 illustrates three groups of frequency-dependence calibrationcomponents, having different modulation frequencies, for use inDetection-System Frequency-Dependence Compensation Analyzer. Calibrationgroup 59.FC.1 comprises three adjacent, concentric radiation filtershaving different modulation frequencies. Calibration group 59.FC.1 issubject to errors resulting from non-constant, non-uniform radialintensity distributions. Calibration group 59.FC.2 comprises threeradiation filters occupying sequential annular segments within a commonannular region. This design is preferable to 59.FC.1, but is subject toerrors resulting from sub-rotational period intensity transients.Calibration group 59.FC.3 comprises three interlaced radiation filtershaving different modulation frequencies. This design is the mostpreferable, as it is substantially immune to non-uniform radialintensity distributions and sub-rotational period intensity transients.

The calibration groups shown in FIG. 15 are intended to be combined withapplication specific patterns; e.g., the optimized Chemometric patternsof the Multivariate Chemometric Analyzer described above. In thismanner, the application specific components can be compensated for thefrequency dependence of detector 26.

In modulator 22FC, the number of filters in each frequency-dependencecalibration group, and the configuration of the annular regions andannular segments was chosen for illustrative purposes, and is notintended to limit the scope of the invention.

Short-Path Post-Encoder Optic

In many applications of analyzer 100 of FIG. 1, there are drivingconcerns that limit the length of the optical path between the modulator22 and detector 26 (or the entrance to a sample cell). For example, ashort optical path is desirable in analyzers that measure spectralcomponents subject to interference in the uncontrolled path. Anothercommon design constraint is the size of the detector element crosssection (or sample-cell cross section), which dictates the maximumallowed spot size of the encoded beam at the surface of detector 26 (orsample-cell aperture). One of the most significant engineeringchallenges of the present invention is the design post-encoder optic 36Bfor embodiments where one or more dimensions of the detector element (orsample cell 38) cross section are substantially smaller than (e.g., lessthan ¼) the length of target image 52 along the radial axis of modulator22. This challenge is compounded in embodiments of analyzer 100 of FIG.1A, where target image 52 is a dispersed image. Preferably, post-encoderoptic 36B is designed such that two or more encoded spectral components(e.g., 56.1 and 56.2 of FIG. 1A) substantially overlap one another onthe surface of the detector element or the entrance to sample cell 38.

In embodiments of analyzer 100 that use a reflective modulator 22, thedetector cross section (or sample cell cross section) constraint leadsto a short-path constraint as well, as the spindle wobble of modulator22 about rotation axis 40 results in the movement of the focused encodercomponents (e.g., 56.1 and 56.2) on the surface of the detector element(or the sample cell entrance). The spindle wobble can lead to anenvelope modulation of the detected radiation (e.g., if there arespatial variations in the responsivity of detector 26), the amplitude ofwhich increases as the optical path length between modulator 22 anddetector 26 increases. If the optical path is too long, encoded beam 56may periodically walk off the detector element entirely, leading toabrupt discontinuities in one or more of the encoded waveforms and acorresponding corruption of the decoded amplitudes. In these and otherapplications, it is desirable to engineer post-encoder optic 36B toprovide a short optical path between modulator 22 and detector 26, andproduce an encoded beam spot on the surface of detector 26, comprisingthe substantially overlapping images of the encoded components.Preferably, the size of the spot is substantially the same as the sizeof the element of detector 26, although the spot size can also besmaller than the size of the element of detector 26. More preferably,the radiation density (illumination) of each of the encoded componentsis substantially uniform over the area of detector 26. In this manner,the effects of spindle wobble on detected signal 27 can be minimized.

In the discussion that follows, we describe two configurations, SP1 andSP2, for a compact, Short-Path post-encoder optic for a 25.6 mm×2.0 mmdispersed image, created with (approximately) F/4 pre-encoder optics(i.e., spectrograph optics), and using a reflective embodiment ofmodulator 22. The dispersion axis of target image 52 is along a radialaxis of modulator 22. The Short-Path post-encoder optic has a totaloptical-path length (on centers) of less than the diameter of modulator22, and focuses a minimum of 20% of each encoded radiation component (oran average of 20% over all encoded components) onto a 3.0 mm×3.0 mmcross sectional area (e.g., a detector element, or a sample cellaperture).

FIG. 16A illustrates one embodiment, Configuration SP1, for a compact,short-path post-encoder-optic for use in spectrum radiation analyzer100. Configuration SP1 was engineered for an embodiment of analyzer 100where detector element 26.SP.1 has a cross section of 3 mm by 3 mm, andtarget image 52 is a dispersed image (in the 3.0 to 5.0 micron spectralrange) having dimensions of 25.6 mm and 2.0 mm, parallel andperpendicular to the dispersion axis, respectively. The SP1configuration for post-encoder optic of analyzer 100, 36B(SP1),comprises the following elements, in sequential order beginning at thetarget image 52 on the surface of modulator 22 and ending at detectorelement 26.SP.1 (in the discussion of SP1 that follows, we do notconsider bandpass filter 26.SP.3 or detector window 26.SP.2):

Configuration 36B(SP1):

-   -   36B(SP1).1: a bi-conic reflector,    -   36B(SP1).2: a planar fold mirror, and    -   36B(SP1).3: a plano-convex focusing lens.

Configuration SP1 has the advantage of exploiting the chromaticdispersion of the focusing lens to provide a smaller encoded beam spoton the surface of detector 26.SP.1, but the spectral range of 36B(SP1)is limited by the transmission properties of 36B(SP1).3. Preferably,36B(SP1).3 is integrated into detector 26.SP.1 so that the transmissionof 36B(SP1).3 can be matched with the spectral responsivity of detector26.

As shown in FIG. 16A, for 36B(SP1), the 128 dispersed radiationcomponents encoded by modulator 22, 56.SP.{1,128}, are collected bybi-conic reflector 36B(SP1).1, reflected by fold mirror 36B(SP1).2, andfocused by lens 36B(SP1).3 onto detector element 26.SP.1. As shown inFIG. 16A, radiation components 56.SP.{1,128} substantially overlap oneanother on the surface of detector element 26.SP.1. The total length ofthe on-centers optical path for 36B(SP1) is roughly 41 mm (i.e., roughly⅔ of the radius of modulator 22).

FIG. 16B shows the collection efficiency vs. wavelength (i.e., theindividual collection efficiencies of the 128 encoded spectralcomponents) for post-encoder optic 36B(SP1) shown in FIG. 16A. Thecollection efficiency is defined as the fraction of radiation in a givenencoded radiation component collected from target image 52 and directedonto detector element 26.SP.1 (i.e., intercepts 26.SP.1). The collectionefficiencies shown in FIG. 16B for configuration SP1 include the effectsof the restricted field of view (FOV) of a commercially available PbSedetector. As shown in FIG. 16B, for configuration SP1, the averagecollection efficiency is greater than 70%, and the range for individualencoded components is between 67% and 89%.

Bi-conic reflector 36B(SP1).1 has an illuminated aspect ratio greaterthan 3:1, and radii of curvature that differ by roughly a factor of two(e.g., 46 mm and 27.5 mm), with the long dimension and long radiusparallel to the dispersion axis. Bi-conic reflector 36B(SP1).1counteracts the dispersion of 52 to provide a focused encoded beam56.SP.{1,128} of substantially overlapping components. Fold mirror36B(SP1).2 is used to reflect the encoded beam away from modulator 22 toprovide room for the placement of detector 26.SP.

FIG. 16C is a side-view of 36B(SP1). As shown in FIG. 16C, fold mirror36B(SP1).2 is located in a plane (shown as the dot dash line) parallelto the plane of modulator 22 (shown as the double-dot dash line). Inorder to minimize the size of 36B(SP1), the plane of fold mirror36B(SP1).2 is parallel and as close to the surface of modulator 22 aspractical; e.g., Δz_(min) is the minimum clearance between modulator 22and 36B(SP1).2 as determined by the brackets and fixtures (not shown)required to position the components of 36B(SP1) relative to modulator22; e.g., Δz_(min) is less than 2 inches.

Focusing lens 36B(SP1).3 is a spherical plano-convex lens with a radiusof curvature of roughly 18 mm, and is used to focus the encoded beamthrough detector window 26.SP.2 onto detector element 26.SP.1.Preferably, the material focusing lens of 36B(SP1).3 is selected toexploit the effects of chromatic dispersion to produce a smaller, moreoverlapping, and/or more uniform encoded beam 56.SP.{1,128} on thesurface of detector element 26.SP.1.

Configuration SP1 for post-encoder optic 36B has a total optical-pathlength (on centers) of 41 mm (i.e., roughly ⅔ of the radius of modulator22).

FIG. 16D illustrates a side-view of a second configuration, SP2, forpost-encoder optic 36B of analyzer 100 that uses two Fresnel bi-conicreflectors in place of the bi-conic mirror, plane mirror and theplano-convex focusing lens of 36B(SP1). Configuration SP2 was alsoengineered for an embodiment of analyzer 100 where detector element26.SP.1 has a cross section of 3 mm by 3 mm, and target image 52 is adispersed image (in the 3.0 to 5.0 micron spectral range) havingdimensions of 25.6 mm and 2.0 mm, parallel and perpendicular to thedispersion axis, respectively. As shown in FIG. 16D, configuration SP2comprises the following elements, in sequential order beginning at thetarget image 52 on the surface of modulator 22 and ending at detectorelement 26.SP.1 (in the discussion of SP2 that follows, we do notconsider bandpass filter 26.SP.3 or detector window 26.SP.2):

Configuration 36B(SP2):

-   -   36B(SP2).1: a Fresnel bi-conic reflector,    -   36B(SP2).2: a Fresnel bi-conic reflector,

Configuration SP2 has the advantage of having one fewer optical elementin the design. Configuration SP2 also has the significant advantage ofbeing comprised entirely of reflective components, which makes it usefulfor a variety of embodiments of analyzer 100 encoding radiation a numberof different wavelength ranges. As shown in FIG. 16D, the facets of36B(SP2).1 are engineered such that it can be located in a plane (shownas the dot dash line) parallel to the plane of modulator 22 (shown asthe double-dot dash line), which significantly simplifies the design andassembly. In order to minimize the size of 36B(SP2), the plane ofFresnel bi-conic reflector 36B(SP2).2 is parallel and as close to thesurface of modulator 22 as practical; e.g., Δz_(min) is the minimumclearance between modulator 22 and 36B(SP2).2 as determined by thebrackets and fixtures (not shown) required to position the components of36B(SP2) relative to modulator 22; e.g., Δz_(min) is less than 2 inches.

Configuration SP2 for post-encoder optic 36B also has a totaloptical-path length (on centers) of roughly ⅔ of the radius of modulator22, and similar collection efficiencies. As shown in FIG. 16D, radiationcomponents 56.SP.{1,128} substantially overlap one another on thesurface of detector element 26.SP.1.

In configurations SP1 and SP2 for Short Path optic 36B, the variousradii of curvature, the facets of the bi-conic Fresnel surfaces, and thespatial configuration of the individual optical elements were optimizedusing the User-Defined Operand (UDO) optimization procedure includedwith the Zemax® optical design program. The UDO optimization featureallows the user to create application-specific merit functions in the‘c’ programming language. The UDO used to optimize the Short Pathconfigurations described above, UDO.SP, uses the Zemax® ray-tracingengine to trace rays from source 24 to detector 26.SP as a function ofwavelength. In UDO.SP, the total merit function, χ_(SP), is given by

$\begin{matrix}{\chi_{SP} = {\chi_{path} + {\sum\limits_{n = 1}^{N_{\lambda}}\chi_{n}}}} & (29)\end{matrix}$where, χ_(path) is the Path-Length Merit Function, the χ_(n) are theWavelength Efficiency Merit Functions, and the summation is over N_(λ)selected spectral components of target image 52.

The Path-Length Merit Function used in UDO.SP is given by

$\begin{matrix}{{\chi_{path} = {\exp\left( \frac{\left( {L_{path} - L_{path}^{0}} \right)}{\sigma_{path}} \right)}},} & (30)\end{matrix}$where L_(path) ⁰ is the target maximum path length, L_(path) is theon-centers optical path length (i.e., through the centers of thetransmissive components, and to and from the centers of the reflectivecomponents of optic 36B) between target image 52 and detector element26.SP.1, respectively, and σ_(path) is an adjustable parameter thatcontrols the penalty for L_(path)>L_(path) ⁰. In the optimization of SP1and SP2, the target maximum path length was selected to be ⅔ the radiusof modulator 22.

The Wavelength Efficiency Merit Functions, which measure the efficiencyof post-encoder optic 36B as a function of wavelength, are given by

$\begin{matrix}{{\chi_{n} = {\exp\left( \frac{\left( {ɛ_{n}^{0} - ɛ_{n}} \right)}{\sigma_{n}} \right)}},} & (31)\end{matrix}$where ε_(n) ⁰ and ε_(n) are the target efficiency and the ray-traceefficiency computed by UDO.SP at the n-th wavelength λ_(n),respectively, and σ_(n) is an adjustable parameter which controls thepenalty for ε_(n)<ε_(n) ⁰. In UDO.SP, detector element 26.SP.1 is givenfinite dimensions (e.g., 3 mm by 3 mm), and a finite field of view (FOV)(e.g., 45 deg.). The efficiency ε_(n) is simply the fraction of rays (ofat λ_(n)) traced from source 24 that intercept detector element 26.SP.1with an angle of incidence less than the specified FOV. In theoptimization of SP1 and SP2, 32 equally spaced wavelengths between 3 and5 microns were traced, and the target efficiencies were all set to 70%.For each wavelength, multiple traces having different points of originand different initial propagation vectors were used to simulate a finitesource 24, and a finite entrance aperture 32.

By a judicious selection of the individual wavelength targetefficiencies, ε_(n) ⁰, post-encoder optic 36B can be optimized tocompensate for the spectral responsivity of detector 26.SP or thespectral efficiency of other optical components of analyzer 100 (e.g.,source 24, pre-encoder optic 36A, etc . . . ). These and othervariations are within the scope of the invention.

UDO.SP has an option to optimize the design of optic 36B to provide amore uniform illumination of the detector element for each spectralcomponent. In this embodiment, UDO.SP substitutes the UniformIllumination Merit Function (χ_(n)) for χ_(n)

$\begin{matrix}{\left\langle \chi_{n} \right\rangle = {\sum\limits_{m}^{N_{m}}\;{\exp\left( \frac{\left( {\frac{ɛ_{n}^{0}}{N_{m}} - ɛ_{n}^{m}} \right)}{\sigma_{n}} \right)}}} & (32)\end{matrix}$where N_(m) is a parameter defining the number of equal-sized regionscomprising the cross-sectional area of detector element 26.SP.1 (i.e.,26.SP.1 is diced up into N_(m) equal-sized regions), and ε_(n) ^(m) isray-trace efficiency computed by UDO.SP at the n-th wavelength and them-th sub-area of detector 26. An embodiment of Short Path post-encoderoptic 36B optimized with (χ_(n)) will have substantially uniformillumination over the cross-sectional area of detector element 26.SP.1.In this manner, the effects of spindle wobble on detected signal 27 canbe minimized.

With suitable substitutes for focusing lens 36B(SP1).3, post-encoderoptic 36B can be used for a generalized class of dispersed images,having substantially identical angles of incidence, lengths, widths, andangles of dispersion. With minor variations, post-encoder optic 36B(SP1)can be incorporated into a wide variety of products based on analyzer100. Since post-encoder optic configuration SP2 is comprised of allreflective components, 36B(SP2) can be incorporated into a wide varietyof products based on analyzer 100, without modification, exploit theeconomics of scale. These and other variations are within the scope ofthe invention.

We note that obvious improvements can be made by introducing additionaloptical elements, non-spherical conic sections, refractive ordiffractive elements, or gradient-index lenses to the design of 36B, andare within the scope of the invention, albeit, with a significantincrease in cost and manufacturing complexity.

The dispersed image size, the pre-encoder optics F/#, the targetefficiency, the position and curvature of the optical elements, themerit functions, and the number of encoded components were chosen forillustrative purposes. Other post-encoder optics, which are designed fortransmissive modulators, different pre-encoder optics, differenton-centers path length, different target efficiencies, different numberof elements, different curvatures, different merit functions, and/orincorporate nonlinear conic section, refractive or diffractive elements,or gradient-index lenses, are within the scope of the invention.

Encoded Filter-Photometer Analyzer

In another embodiment of analyzer 100 depicted in FIG. 1, EncodedFilter-Photometer Analyzer is a multi-channel-encoder filter-photometerthat uses one or more broadband radiation sources and a collection(e.g., an array) of wavelength filters to provide a plurality of encodedspectrally filtered beams for probing one or more unknown samples.

In Encoded Filter-Photometer Analyzer, radiation from source 24 isfiltered by a collection of wavelength filters to provide a firstplurality of selected spectral components. Examples of sources includeextended sources, multi-filament lamps, and an array of blackbodyradiators. Examples of wavelength filters include multi-dielectric-layerbandpass filters, etalons and dichroic mirrors (e.g., stacked ½ and ¼wave plates). Further examples of wavelength filters include radiometrycorrelation cells filled with various gasses or liquids. Furtherexamples of wavelength filters include optical elements incorporatingone or more partially transparent (or partially reflective) solids. Suchand other examples of sources and wavelength filters, are within thescope of the invention.

Preferably, the collection of wavelength filters includes both analyteand reference wavelength filters to provide a first plurality of analyteand reference beams. Examples of analyte beams include radiationfiltered by CO, CO₂, NO_(x), N₂O, H₂O, H₂S, solvents and varioushydrocarbons, including the constituents of natural gas. Due to theinherent danger, radiation filtered by chemical weapons and other toxicgasses and liquids make less practical examples of analyte beams.Further examples of analyte beams include radiation filtered by one ormore multi-dielectric-layer bandpass filters or dichroic mirrors wherethe selected spectral components are engineered to substantiallycoincide with one or more significant spectral features of acorresponding analyte; e.g., the analyte beams comprise one or moreoptimized spectral components of Multivariate Chemometric Analyzer.Examples of reference beams include radiation filtered by N₂, water, asolvent, or full or partial vacuum. Further examples of reference beamsinclude radiation filtered by one or more multi-dielectric-layerbandpass filters where the selected spectral components are engineeredto minimize the coincidence with any significant spectral features ofall analytes potentially in the sample.

The radiation filtered through the collection of wavelength filters isimaged with pre-encoder optic 36A to form target image 52 substantiallyalong a radial axis of modulator 22. Target image 52 comprises a firstplurality of sub-images corresponding to the radiation transmittedthrough the wavelength filters, which are focused (or centered) atsubstantially different radial positions along one or more radial axesof modulator 22. Modulator 22 has a number of radiation filters atdifferent radii for encoding target image 52 to provide a secondplurality of encoded beams as modulator 22 is rotated about rotationaxis 40. Preferably, the sub-images are aligned with the radiationfilters such that the encoded beams have a substantially one to onecorrespondence with the radiation transmitted through the individualwavelength filters.

Preferably, the encoded analyte and reference beams are propagatedthough (or reflected from) one or more samples. Examples of samplesinclude ambient air, automobile exhaust, a process stream, the internalair of a cargo container, a HVAC intake, ductwork or exhaust, andnatural gas. If the sample is a gas or liquid, it is preferred that thesample be bounded by a sample cell. Further examples of samples includetransmissive and reflective solids.

In one embodiment of Encoded Filter-Photometer Analyzer, multiple samplecells are used to provide multiplexing from multiple gas and/or liquidsamples. The configuration of pattern 21 and post-encoder optic 36B areengineered to provide application-specific groups of analyte-referencebeam pairs to each of the sample cells. For example, the first samplecell contains two unknown analyte concentrations—and employs at leasttwo analyte-reference beam pairs for the analysis, and the second samplecell contains five unknown analyte concentrations—and employs at leastfive analyte-reference beam pairs for the analysis. If the applicationcalls for two or more samples to be probed with identicalanalyte-reference beam pairs, multiple detectors and ADCs can be used asdescribed below. In this manner, multiple samples can be probedsubstantially simultaneously.

After propagating through the sample, the encoded correlation beams arecollected, directed, and focused by post-encoded optic 36B onto detector26, and computer 28 analyzes the signals generated by detector 26 inresponse to the encoded beams to determine the amplitudes of the encodedcomponents. The amplitudes of the encoded components are subsequentlyused by application specific algorithm 28.asf to determine the presenceand concentrations of one or more analytes in the sample.

Preferably, the analyte and reference beams (and their respective targetsub-images) are configured as pairs in sequence along the radial axis ofmodulator 22 (i.e., each analyte beam is adjacent to a correspondingreference beam), or symmetric with respect to one or more symmetry radii(i.e., each analyte beam is mirrored to a corresponding reference beamabout one or more symmetry radii), to comprise a analyte-reference pairhaving substantially identical optical paths within the sample, and/orsubstantially identical normalized intensity distributions on thesurface of detector 26. More preferably, the analyte and reference beamsof a given pair are encoded with a complementary filter pair, such thatthe amplitude and phase of the resulting encoded component aredetermined by the relative intensity of the analyte and reference beams.Most preferably, the relative modulation intensity of the complementaryfilters are engineered (e.g., by inserting an aperture or a neutraldensity filter in the path of the corresponding reference beam, or byvarying the width or modulation depth of the radiation filter encodingthe reference beam with respect to the radiation filter encoding theanalyte beam) to null the resulting encoded component in the absence (ora nominal level) of a correlating absorption in the sample cell. In thismanner, Encoded Filter-Photometer Analyzer provides a filteredphotometric measurement of the highest photometric accuracy.

Preferably, the spectral range of each analyte-reference beam pair islimited (e.g., by one or more dichroic mirrors, bandpass filters, and/orcells filled with various gasses or liquids, including one or moreconstituents of natural gas), to isolate one or more significantspectral features of the analyte, or exclude one or more significantspectral features of one or more different (other) analytes. In thismanner, the sensitivity (e.g., the amplitude of the encodedanalyte-reference pair in response to a given concentration of theanalyte in the sample cell), and/or the specificity (e.g., the abilityto discriminate between two or more analytes) of the instrument to theanalytes in the sample can be enhanced. For example, a cell filled withmethane (the dominant constituent of natural gas) can be used to excludethe spectral features of methane in reference filtered components andnon-methane analyte filtered components used in the analysis of naturalgas.

The path of a given encoded beam through the system (including thesample or correlation cell) is actually a superposition of the pathsfrom all optical ray traces which begin at source 24, reflect from theactive area of the corresponding radiation filter on modulator 22, andreach detector 26. As a consequence, the superposition of paths changesas the pattern of the radiation filter within the active area changes asmodulator 22 rotates. In the presence of absorbing analytes where theattenuation of the beam depends of the path length, the variation in thesuperposition of the paths can lead to a waveform distortion of anencoded component. In the present invention, these effects can beminimized by reducing the number of abrupt discontinuities along one ormore axes in the pattern of the radiation filters. Preferably, theradiation filters of modulator 22 comprise the “bar-code” or“checker-board” like patterns described above to provide one or moreencoded components with a substantially constant superposition ofoptical paths through the system.

FIG. 17A is a schematic top view of an embodiment of EncodedFilter-Photometer Analyzer, which encodes radiation filtered by twoanalyte-reference correlation-cell pairs, {F.A₁, F.R₁}, and {F.A₂,F.R₂}, respectively. Correlation cell F.A₁ and correlation cell F.A₂ arefilled with known concentrations of analytes A₁ and A₂, respectively. Asshown in FIG. 17A, radiation is provided by two broadband ormulti-spectral component radiation sources, 24.FP.1 and 24.FP.2.Radiation from source 24.FP.1 is collected and focused by pre-encoderoptic 36A(FP).2.1 (e.g., a first lens pair) to form target sub-images52.FP.A₁ at a first point along a radial axis of modulator 22FP, and52.FP.R₁ at a second point along a radial axis of modulator 22FP.Similarly, Radiation from source 24.FP2 is collected and focused bypre-encoder optic 36A(FP).2.2 (e.g., a second lens pair) to form targetsub-image 52.FP.A₂ at a third point along a radial axis of modulator22FP, and 52.FP.R₂ at a fourth point along a radial axis of modulator22FP. The target sub-images (52.FP.A₁, 52.FP.R₁, 52.FP.A₂ and 52.FP.R₂)and the corresponding radiation sources (24.FP.1 and 24.F.P2) comprisetarget image 52 and radiation source 24, respectively.

As shown in FIG. 17A, pre-encoder optic 36A(FP) includes bandpass filter36A(FP).1.1 to limit the spectral range of analyte-reference beam pair{56.A₁, 56.R₁} to isolate one or more significant spectral components ofanalyte A₁, and bandpass filter 36A(FP).1.2 to limit the spectral rangeof analyte-reference beam pair {56.A₂, 56.R₂} to isolate one or moresignificant spectral components of analyte A₂. For example, the bandpassfilters are engineered to coincide with two of the optimized spectralwindows of the Multivariate Chemometric Analyzer. In this manner, theamplitude change of the encoded analyte-reference pair in response to agiven concentration of the analyte in the sample (i.e., the sensitivity)can be enhanced.

In an alternative embodiment of Encoded Filter Photometer shown in FIG.17A, bandpass filter 36A(FP).1.1 or 36A(FP).1.2 can be replaced with acell filled with various gasses, liquids or solids (e.g., one or moreconstituents of natural gas), to exclude one or more significantspectral features of one or more different (other) analytes. In thismanner, the specificity (e.g., the ability to discriminate between twoor more analytes) of the instrument to the analytes in the sample can beenhanced. For example, a cell filled with methane (the dominantconstituent of natural gas) can be used to exclude the spectral featuresof methane in reference filtered components and non-methane analytefiltered components used in the analysis of natural gas.

A schematic side view of Encoded Filter-Photometer Analyzer is shown inFIG. 17B to further illustrate the path of beam 56.A₁ from source24.FP.1 to detector 26. As shown in FIG. 17B, radiation from source24.FP.1 is filtered by bandpass filter 36A(FP).1.1 and collected andfocused by pre-encoder optic 36A(FP).2.1 to form sub-image 52.FP.A₁ onthe surface of modulator 22FP. As modulator 22FP is rotated aboutrotation axis 40, sub-image 52.FP.A₁ is sequentially encoded byradiation filter 50.FP1 and complementary radiation filter pair 55.FP1to provide encoded beam 50.A₁. Encoded beam 50.A₁ is collected bypost-encoder optic 36B(FP).1.1 and directed through correlation cellF.A.sub₁, which contains a known concentration of analyte A₁. Afterpropagating through correlation cell F.A₁, the encoded beam 56.A₁ iscollected by post-encoder optic 36B(FP).2.1 and directed though samplecell 38.FP. After propagating through sample cell 38.FP, encoded beam56.A₁ is collected by post-encoder optic 36B(FP).3 and focused ontodetector 26.

As shown in FIG. 17A, the analyte and reference cells, F.A₁, F.R₁, F.A₂,and F.R₂, of Encoded Filter-Photometer Analyzer are configured such thateach analyte beam is adjacent to a corresponding reference beam, tocomprise an analyte-reference beam pair having substantially identicalpaths within sample cell 38.FP, and/or substantially identical intensitydistributions on the surface of detector 26. More preferably, theanalyte and reference beams of a given pair are encoded with acomplementary filter pair, such that the amplitude and phase of theresulting encoded component are determined by the relative intensity ofthe analyte and reference beams. Most preferably, the relativemodulation amplitude of the complementary filters are engineered (e.g.,by inserting an aperture or a neutral density filter in the path of thecorresponding reference beam, or by varying the width or modulationdepth of the reference filter with respect to the analyte filter) tonull (e.g., by imposing comparable amplitudes for analyte and referencebeams) the resulting encoded component in the absence (or a nominallevel) of a correlating absorption in the sample cell.

In FIG. 17, the order of the optical elements was chosen forillustrative purposes and is not intended to limit the scope of theinvention. For example, the position of the analyte and reference cellarray with respect to the encoder is arbitrary. The radiationtransmitted through the correlation cells can be encoded or theradiation can be encoded and then transmitted through the correlationcells. In addition, the sample cell can be placed anywhere betweensource 24 and detector 26 in the beam path. These and other variationsare within the scope of the invention.

In reference to FIG. 9, for Encoded Filter-Photometer Analyzer describedabove, the position of the collection of spectrally filtered sub-images,the position of the array of analyte and reference wavelength filters,the position of the sample cell(s), and/or other optical elements, canbe controlled to align target image 52 onto modulator 22, and align theencoded correlation beams to pass through the sample cell(s) onto thedetector. As shown in FIG. 17A, all of the optical components can bepre-aligned, and mounted on a common stage, 35.FP, which can be movedrelative to modulator 22FP to align target image 52.FP. Preferably,source 24.FP includes a number of alignment spatial components andmodulator 22FP includes a number of alignment channels to provide inputto the Alignment Calibration Algorithm 28.utl(ACA), which in turn,generates one or more control signals to position one or more opticalelements (e.g., 35.FP) to align target image 52.FP onto modulator 22FP.

Preferably, pre-encoder optic 36A(FP) is engineered to provide analyteand reference sub-images (e.g., 52.FP.A₁, 52.FP.R₁, 52.FP.A₂ and52.FP.R₂) at different radial positions along different radial axes.More preferably, the mechanical fixtures (brackets) used to position theindividual elements of pre-encoder optic 36A(FP) (e.g., bandpassfilters, sources, lenses) are engineered (e.g., by locatinganalyte-reference correlation-cell pairs at different radial positionsand along different radial axes) to minimize the radial separationbetween analyte-reference pair sub-images (e.g., {52.FP.A₁, 52.FP.R₁},and {52.FP.A₂, 52.FP.R₂}).

Preferably, the position of the individual filaments and the position ofthe individual radiators are engineered in conjunction with theplacement of radiation filters to simplify the design of pre-encoderoptic 36A(FP); e.g., match the pitch of the filaments and/or radiatorsto the pitch of the radiation filter pairs on modulator 22.

Phase-Locked Noise-Rejection Analyzer

In many applications of analyzer 100 of FIG. 1, there are one or moresubstantially periodic noise sources in the system (e.g., source drivecurrent, switching power supplies, 60 Hz line, back-EMF from motors andcooling fans, etc . . . ) that corrupt the encoded signal digitized by28.adc. Without active phase locking, the phase of the periodic noisesource drifts with respect to the phase of the encoded radiationcomponents, leading to an unpredictable corruption of the decodedamplitudes. If the phase of the noise source is phase-locked withrespect to the rotation of the modulator, the corruption of thedigitized encoded signal can be minimized or significantly eliminated bythe judicious selection of the encoding harmonics.

In another embodiment of analyzer 100, Phase-Locked Noise-RejectionAnalyzer includes a Noise Search Algorithm, 28.utl(NSA) and a NoisePhase Locking Algorithm, 28.utl(NPL), to phase-lock the rotation ofmodulator 22 to one or more periodic noise sources in order to minimizethe corruption of the encoded components.

FIG. 18 is a schematic illustration of Phase-Locked Noise-ReductionAnalyzer. As shown in FIG. 18, modulator 22 includes radiation filtersto encoded radiation from source 24, to provide an encoded beam 56.PL asmodulator 22 rotates about rotation axis 40. The modulation functions ofthe radiation filters are engineered to be harmonics of the rotationperiod of modulator 22. As such, the encoded beam comprises a set ofencoded harmonics, 56.PL.1, 56.PL.2, and 56.PL.3. Encoded beam 56.PL isdirected to detector 26 by post-encoder optic 36B, and computer 28analyzes signal 27 generated by detector 26 in response to encoded beam56.PL and corrupted by one or more substantially periodic noise sources,29.

As shown in FIG. 18, computer 28 includes a Motor Control Algorithm28.utl(MCA) and a digital-to-analog converter 28.dac to vary the speedof motorized spindle 42. In addition to decoding encoded components56.PL.{1,2,3}, computer 28 decodes the amplitude and phases of a set ofnoise-tracking harmonics, which are also harmonics of the rotationperiod of modulator 22, but are not in the set of encoded harmonics. Thenoise tracking harmonics are provided to 28.dec by Noise SearchAlgorithm 28.utl(NSA). Preferably, the set of noise-tracking harmonicsare interspersed with encoding harmonics of 56.PL.{1,2,3} to enable28.utl(NSA) to better detect periodic noise source 29. More preferably,set of noise-tracking harmonics substantially correspond to theanticipated frequencies of one or more periodic noise sources (e.g., 29)at one or more default (or ideal) speeds of motorized spindle 42.Preferably, if periodic noise source 29 contains overtone harmonics(e.g., the periodic noise source is a square wave having odd-harmonicovertones), the set of encoding radiation filters providing 56.PL.{1,2,3} is engineered to omit the fundamental and one or more significantovertones of phase-locked periodic noise source 29.

At start-up, and whenever necessary thereafter, Noise Search Algorithm28.utl(NSA) systematically varies the speed of motorized spindle 42(e.g., by sending commands to 28.utl(MCA)), and 28.dec decodes theamplitude and phase of the noise-tracking harmonics until a spindlemotor speed is found that maximizes the decoded amplitude of one or morenoise-tracking harmonics. Computer 28 then uses the amplitude and phaseof the dominant noise-tracking harmonic as input to Noise Phase LockingAlgorithm (e.g., a phase-locked loop), 28.utl(NPL), which outputs acontrol signal to 28.utl(MCA), which controls the speed of motorizedspindle 42 via 28.dac to stabilize or lock the phase of the dominantnoise-tracking harmonic. In this manner, periodic noise source 29 isphase-locked with respect to the rotation of modulator 22, andtherefore, is rendered substantially orthogonal to encoded components56.PL.{1,2,3}.

In one embodiment of Phase-Locked Noise-Reduction Analyzer, the speed ofmotorized spindle 42 is synchronized with one or more pneumatic pumps ina closed-loop sampling system. In this manner, artifacts resulting frommass-density oscillations driven by the pneumatic pump can be minimized,compensated for, or analyzed.

Pattern-Concentricity Analyzer

One of the most critical tasks in the assembly of analyzer 100 is themounting of modulator 22 onto motorized spindle 42. For the analyzer tooperate properly, pattern 21 on modulator 22 must be substantiallyconcentric with the axis of rotation 40. If modulator pattern 21 is notconcentric with rotation axis 40, the selected radiation components willexperience an unwanted secondary modulation as the annular regions ofthe radiation filters oscillate back and forth along the radial axis asmodulator 22 is rotated about rotation axis 40.

In another embodiment of analyzer 100, Pattern-Concentricity Analyzergauges the concentric alignment (i.e., the concentricity) of pattern 21on modulator 22 with respect to axis of rotation 40. InPattern-Concentricity Analyzer, pre-encoder optic 36A forms the targetimage of at least one alignment radiation component (e.g., the image ofa He—Ne laser beam) onto an encoding plane along an encoding axis.Modulator 22 is located in the encoding plane and includes at least onecomplementary filter pair to provide an encoded alignment beam asmodulator 22 is rotated about rotation axis 40. Preferably, theradiation filters comprising the alignment filter pair are substantiallyadjacent to one another. More preferably, the radial width of thealignment filter pair is substantially equal to the width of thealignment target image. Most preferably, the width of the image of thealignment component (i.e., the alignment target image) is twice as largeas the maximum anticipated displacement of the center of modulatorpattern 21 with respect to axis of rotation 40.

FIG. PCA is a schematic illustration of Pattern-Concentricity Analyzer,which gauges the concentric alignment of modulator pattern 21 PC withrespect to rotation axis 40. Radiation source 24.PC provides at leastone radiation component for probing the concentricity of pattern 21PC.Pre-encoder optic 36A collects radiation from source 24.PC and formstarget image 52.PC on the surface of modulator 22PC. As shown in FIG.PCB, in addition to application specific radiation filters and filterpairs (not shown), modulator 22PC includes complementary radiationfilter pair 55.PC (comprising 50.PC.1 and 50.PC.2) to encode targetimage 52.PC as modulator 22PC rotates about rotation axis 40. As shownin FIG. PCA, encoded beam 56.PC is collected by post-encoder optic 36Band directed onto detector 26.PC. Preferably, radiation source 24.PC issufficiently collimated as to make optics 36A and 36B unnecessary.Computer 28 analyzes the signals generated by detector 26.PC in responseto encoded alignment beam 56.PC to determine concentricity of modulatorpattern 21PC with respect to rotation axis 40.

FIG. PCB illustrates the difference between the center of the modulatorpatter, 21PC.0, and rotation axis 40. The vector displacement of patterncenter 21PC.0 relative to rotation axis 40 is defined as theconcentricity error. Modulator pattern 21PC is said to be concentricwith respect rotation axis 40 in the limit where the concentricity errorgoes to zero.

For the discussion that follows, we define the ideal border radius,R_(PC), as the radial position of the border between 50.PC1 and 50.PC2when modulator pattern is concentric with respect to rotation axis 40.Preferably, pre-encoder optics 36A substantially positions alignmenttarget image 52.PC in the encoding plane at ideal border radius R_(PC).

As shown in FIG. PCA, radiation source 24.PC, pre-encoder optics 36A,post-encoder optics 36B, and detector 26.PC are mounted on translationstage 35.PC.1, aligned substantially parallel to the radial axis ofmotorized spindle 42, to allow one to precisely position alignmenttarget image 52.PC on the surface of modulator 22PC at ideal borderradius R_(PC).

Computer 28 includes Pattern Concentricity Algorithm, 28.utl(PCA), whichanalyzes the amplitude and phase of encoded alignment component 56.PC asa function of the rotation angle to determine the displacement vector ofthe center of modulator pattern 21PC with respect to rotation axis 40.For example, if the alignment component is centered at the ideal borderradius, the amplitude of encoded alignment component 56.PC is nulledwhen modulator patter 21PC is concentric with respect to rotation axis40. If pattern 21PC is not concentric with respect to rotation axis 40,the sign of the phase change and the angular positions of the amplitudezero-crossings of the encoded alignment component provide all of theinformation needed to determine the displacement vector of the center ofmodulator pattern 21PC with respect to axis of rotation 40. If themagnitude of the displacement vector is less than one-half the width ofthe image of the alignment component, the magnitude of the displacementvector is substantially proportional to the maximum amplitude of theencoded alignment component.

Preferably, pattern-spindle concentricity Pattern-Concentricity Analyzeris combined with actuator mechanism 35.PC.2 for moving modulator intoplace. As shown in FIG. PCA, computer 28 includes a control signal fromhardware driver to actuator mechanism 35.PC.2. Actuator mechanism35.PC.2 includes contact probe 35.PC.2.1 for moving modulator 22PC alongthe radial axis. Computer 28 moves the contact probe in response to theangular dependence of encoded alignment component 56.PC. The processcontinues until the amplitude of encoded alignment component 56.PC issubstantially independent of the rotation angle of modulator 22PC,preferably zeroed. As an alternative to using actuator mechanism35.PC.2, 28.utl(PCA) can used to control audio or optical signals toprovide an assembly technician with feedback as modulator pattern 21PCis hand positioned (e.g., tapped) into substantial concentric alignment.

Preferably, pattern-spindle concentricity Pattern-Concentricity Analyzeris combined with a mechanism for securing modulator 22 to motorizedspindle 42 (e.g., using a UV-curing epoxy and a triggered flash lamp).As shown in FIG. PCA, motorized spindle includes epoxy seat 42.2 whichis covered with a UV-curing epoxy. Modulator disc 22PC is placed on topof epoxy seat 42.2, and the alignment process begins. Once modulatorpattern 21PC is substantially concentric with respect to rotation axis40 (e.g., the concentricity error is similar to the radial run-out ofmotorized spindle 42), a UV lamp is triggered to cure the epoxy andsecure modulator 22PC onto motorized spindle 42.

Preferably, motorized spindle 42 and modulator 22PC can be removed fromPattern-Concentricity Analyzer and installed into other embodiments ofanalyzer 100. In this manner, source 24.PC, pre-encoder optic 36A.PC,post-encoder optic 36B.PC, detector 26.PC, computer 28 and mechanisms35.PC.1 and 35.PC.2 comprise an assembly tool (e.g., a centeringstation).

EXAMPLES

The present invention will be further described by the followingexamples, which should be referenced to analyzer 100 of FIG. 1A, unlessstated otherwise. For easier reference, embodiments described below inthe examples of a particular element or system in FIG. 1A or otherfigures herein are typically given composite symbols, such as the numberof the element in FIG. 1A or other figures herein, followed by a decimalpoint and a number or followed by letters. For example, 100.1 is thenumber in an example below of one embodiment of the analyzer 100, wherethis embodiment is different from another embodiment 100.2 of theanalyzer 100. Where an embodiment includes more than one components, thecomposite symbol comprises the number of the element in FIG. 1A or otherfigures herein, followed by a decimal point, a first number or lettersindicating an embodiment of the element, and followed by another decimalpoint and a second number to indicate a particular component of suchembodiment. In example 1, for example, 36B.1.1 and 36B.1.2 indicate thefirst and the second components respectively of the first embodiment ofpost-encoder optic 36B in FIG. 1A or other figures herein. Thesecomposite symbols are not shown in FIG. 1A or other figures herein tosimplify the figures. Additional components introduced by the exampleswill be given unique symbols.

These examples are intended to embody the invention but not to limit itsscope. In all of the examples described below, it is preferred that eachof the modulation functions are smooth functions or digitized replicasof smooth functions having three or more distinct levels of contrast asthe spatial radiation modulator is rotated about rotation axis 40. Mostpreferably, the modulation functions are of the form sin²(mθ+pπ/4).

Example 1

The first example of the multi-purpose analyzer 100 depicted in FIG. 1A,analyzer 100.1, is a multi-spectral-component encoded source with ahigh-intensity, collimated beam, which is used to measure radiationabsorbing gasses and vapors in one or more long, open paths, such asgasses and vapors in FIG. 1A at 38 where the gasses and vapors are notconfined by any enclosure. Examples of long, open paths include theatmosphere, the restricted air space between microwave transceivers, theline of sight between buildings or highway overpasses, between remoteobjects on the battlefield, and along the perimeter of a militarycompound or industrial facility. Radiation source 24.1 is a collimatedradiation beam having a plurality of selected spectral components (e.g.,a carbon dioxide laser). Pre-encoder optic 36A.1 includes at least onediffractive or refractive element to separate the selected spectralcomponents to form target image 52.1 along a radial axis of modulator22.1. Preferably, pre-encoder optic 36A.1 includes a variable attenuatorto precondition or preset the intensities of the selected components.Target image 52.1 is a dispersed image comprising selected spectralcomponents focused at substantially different points along one or moreradial axes of modulator 22.1. Modulator 22.1 includes a number ofradiation filters that encode the selected spectral components toprovide an encoded beam comprising a plurality of encoded spectralcomponents as modulator 22.1 is rotated about rotation axis 40.Preferably, target image 52.1 is aligned with the radiation filters suchthat the encoded components have a substantially one to onecorrespondence with the selected spectral components. Preferably, afirst post-encoder optic 36B.1.1 includes at least one diffractive orrefractive element to substantially re-collimate the encoded components(e.g., 36A.1 and 36B.1.1 comprise at least one grating pair, prism pairor prism-grating combination). In this manner, the encoded beam can bepropagated over a long, open path to a remote reflector or varioustarget objects providing diffuse or specular reflectance and directedback to detector 26.1. Examples of remote reflectors include aretro-reflector, a simple mirror, a satellite, or various target objectsproviding diffuse or specular reflectance. A second post-encoder optic,36B.1.2 (not shown in FIG. 1A), collects the encoded radiation beam anddirects it back to detector 26.1. Computer 28.1 analyzes the signalgenerated by detector 26.1 in response to the encoded beam to determineamplitudes of the encoded components. In this manner, the spectraltransmission properties of the open path between analyzer 100.1 and theremote reflector can be used as input to a Chemometric analysis toprovide a chemical composition analysis of the long, open path; e.g., todetect flammable or toxic chemical, including chemical and biochemicalweapons.

In a related embodiment of analyzer 100.1, the encoded beam ispropagated over a long distance to at least one remote detector RD26.1(similar to detector 26.1, but located at a remote location) shown indotted lines in FIG. 1A. To simplify FIG. 1A, the optic for conveyingthe encoded beam to the remote detector RD26 is not shown. Preferably,the signals generated by RD26 in response to the encoded beam are sentback (not shown) to analyzer 100.1 for analysis by computer 28.1, whichdetermines the amplitudes of the encoded components. More preferably,remote detector RD26 is augmented by a remote computer RC28 to comprisea remote receiver, and the timing and alignment signals are dispatched(e.g., via microwave signal, fiber optic or one or more additionalencoded laser beams) to the remote receiver such that the detectorsignal can be analyzed at the remote location by RC28. Most preferably,the encoded beam is split up with a beam splitter and distributed alongwith the timing and alignment signals to a number of remote receivers.In this manner, the detector signals can be analyzed at each of theremote locations to provide substantially simultaneous spectral analysisin a number of different sample paths (e.g., in grid, perimeter,elevation, and/or fan-out patterns).

In another embodiment of analyzer 100.1, the collimated, encoded beam islaunched into an optical fiber, waveguide, light pipe or purged (orevacuated) tubing and distributed to one or more remote samplingstations such that the uncontrolled path of the encoded beam issubstantially limited outside of the remote sampling station.Preferably, each of the remote sampling stations include at least oneremote detector RD26.1 and a remote computer RC28 (with the samedecoding functionality as computer 28) for analyzing the signalsgenerated by the detector and the timing and alignment signals. In thismanner, the data acquired at the remote locations can be properlyanalyzed.

Preferably, pre-encoder optic 36A.1 and post-encoder optic 36B.1.1 canbe substantially simplified by engineering source 24.1 to provideselected components spatially separated from one another (e.g., spatialvariations in the gain medium or replace the partial mirror of a laserwith a patterned array of dichroic mirrors). More preferably, source24.1 is engineered to provide selected components at spatial locationsthat substantially match the pattern of radiation filters and filterpairs on modulator 22.1.

In reference to FIG. 9A. for the analyzer described above, the positionof one or more optical element can be controlled to align target image52.1 onto modulator 22.1. Preferably, modulator 22.1 includes one ormore alignment radiation filters or filter pairs to encode one or morealignment components of source 24.1. The alignment components provideinput to the Alignment Calibration Algorithm 28.utl(ACA).1, which inturn, generates one or more control signals to position one or moreoptical elements to properly align target image 52.1 onto modulator22.1.

Example 2

The second example of the multi-purpose analyzer 100 depicted in FIG.1A, analyzer 100.2, is a compact spectrum analyzer which uses acollection of bandpass filters or a linear variable filter (LVF) toprovide a plurality of selected radiation components. In analyzer 100.2,the radiation source comprises a broad band or multi-wavelength sourcefiltered by a linear array of two or more bandpass filters (or a lineararray of two or more correlation radiometry filters; e.g., a collectionof physical gas or liquid samples) or a linear variable filter (LVF).Taken together the radiation source and the collection of bandpassfilters or LVF comprise extended source 24.2, having a number of spatialcomponents corresponding to the radiation transmitted through (orreflected from) the individual bandpass filters or specific positionsalong the LVF. The radiation filtered by the array of bandpass filtersor LVF is imaged by pre-encoder optic 36A.2 to form target image 52.2substantially along a radial axis of modulator 22.2. Target image 52.2comprises the sub-images of the radiation transmitted through (orreflected from) the collection of different bandpass filters or selectedportions of LVF focused at substantially different points along saidradial axis of modulator 22.2. Modulator 22.2 has a number of radiationfilters at different radii for encoding the spatial components toprovide an encoded beam as modulator 22.2 is rotated about the rotationaxis 40. Preferably, the spatial components are aligned with theradiation filters such that the encoded components have a substantiallyone to one correspondence with the radiation transmitted through theindividual bandpass filters or selected portions of the LVF. The encodedbeam is collected, directed and focused with post-encoder optic 36B ontodetector 26. Computer 28 then analyzes the signal generated by detector26 in response to the encoded beam to determine the amplitudes of theencoded components. A sample or sample cell (e.g., sample 38 shown as adashed line box in FIG. 1A) can be inserted between the source 24.2 anddetector 26. In this manner, the spectral properties of a sample can bemeasured.

In reference to FIG. 9A. for the analyzer 100.2 described above, theposition of the collection of bandpass filters or LVF (and/or otheroptical elements) can be controlled to align target image 52.2 ontomodulator 22.2. Preferably, extended source 24.2 includes a number ofalignment spatial components (e.g., a non-transmitting mask whichobscures the border between individual bandpass filters or selectedportions of the LVF) and modulator 22.2 includes a number of alignmentchannels to provide input to the alignment calibration algorithm28.utl(ACA).2, which in turn, generates one or more control signals toposition one or more optical elements to align target image 52.2 ontomodulator 22.2.

Example 3

The third example of the multi-purpose analyzer 100 depicted in FIG. 1A,analyzer 100.3, is a spectrum analyzer, which is used for both analyzingand providing feedback to simultaneously control the center wavelengthsof a number of tunable radiation sources. Radiation source 24.3comprises a plurality of spectral components, where each spectralcomponent corresponds to a distinct radiation source and ischaracterized by an intensity and a center wavelength. For example,radiation source 24.3 may be an optical fiber containing a plurality ofoptical signals, where each signal corresponds to a different radiationsource. Radiation emitted by source 24.3 is imaged by pre-encoder optic36A.3 to form a target image 52.3 onto modulator 22.3. Target image 52.3comprises a plurality of sub-images focused at substantially differentpoints along a radial axis of modulator 22.3, where each sub-imagecorresponds to a distinct radiation source. Pre-encoder optic 36A.3comprises at least one diffractive element such that a change in thecenter wavelength of any one of the distinct radiation sources willcause the corresponding sub-image to move substantially along the radialaxis of modulator 22.3. Modulator 22.3 has a number of radiation filterpairs (similar to 55.1 in modulator 22D of FIG. 7) at different radiifor encoding the spectral components to provide an encoded beam asmodulator 22.3 is rotated about rotation axis 40.3. The radiation filterpairs each comprise radiation filters having modulation functions thatare complementary or out of phase so that the amplitude and phase of theencoded component is determined by the relative proportion of radiationincident on the two filters. The encoded beam is collected, directed andfocused by post-encoder optic 36B.3 onto detector 26.3 and computer 28.3analyzes the signals generated by the detector in response to theencoded beam. Computer 28.3 computes the amplitudes and phases of theencoded components from the signals generated by detector 26.3 inresponse to the encoded beam. Preferably, computer 28.3 generates anumber of distinct control signals for adjusting the center wavelengthsof the distinct radiation sources in response to the signals generatedby detector 26.3 to tune the sources. Preferably, the radiation filterscomprising each pair are substantially adjacent to one another, and theborder between the adjacent radiation filters is substantially locatedat the radius which correspond to the radial position of a correspondingsub-image for the nominal or desired center wavelength for thecorresponding tunable radiation source. In this manner, the amplitudesof the encoded components are zeroed (or nulled) when the centerwavelengths of the radiation sources are tuned to the nominal or desiredcenter wavelengths. Any deviation of a given tunable source from thepreferred configuration results in a signal (in its correspondingmodulation channel) in which the sign and amplitude of the decodedsignal indicates the direction and magnitude of the displacement of thecenter wavelength, respectively. In such manner, the decoded signal canbe used as a feedback mechanism to preserve the tunable sources in theoptimum configuration. Thus, where temperature or other environmentalchanges cause the center wavelength to drift, the decoded signal may beused for tuning the tunable radiation source in order to maintain astable and constant center wavelength, such as by changing thetemperature or current of the source.

In reference to FIG. 9A. for the analyzer 100.3 described above, theposition of one or more optical elements can be controlled to aligntarget image 52.3 onto modulator 22.3. Preferably, source 24.3 includesa number of alignment spectral components (e.g., a reference laser or anumber of lines of a gas or impurity spectrum) and modulator 22.3includes a number of alignment channels to provide input to thealignment calibration algorithm 28.utl(ACA).3, which in turn, generatesone or more control signals to position one or more optical elements toalign target image 52.3 onto modulator 22.3.

Preferably, the intensities of the distinct radiation sources aremeasured from time to time. For this purpose, 28.utl(ACA).3 can be usedto generate one or more control signals to reposition one or moreoptical elements to move target image 52.3 along the radial axis fromits default position to a detuned position. This in turn collectivelymoves the sub-images corresponding to the individual radiation sourcesalong the radial axis. Computer 28.3 would then compare the decodedamplitudes obtained from the default position of target image 52.3 tothe decoded amplitudes obtained from the detuned position of targetimage 52.3 to determine the intensities of the distinct radiationsources. More preferably, an array of patterns similar to {55.3, 50.22},and {55.4, 50.23} shown in modulator 22E of FIG. 8 are used to allow oneto measure both the center wavelength and the total intensity (i.e., thespectral intensity distribution) of each encoded radiation componentwithout detuning the position of target image 52.3.

Example 4

The fourth example of the multi-purpose analyzer 100 depicted in FIG.1A, FIG. 1A, analyzer 100.4, is a fluorescence imaging analyzer with thespeed and sensitivity of a PMT. Radiation source 24.4 is an extendedsource comprising the emission from a collection of differentfluorescent samples. For example, the lanes of a multi-laneelectrophoresis or the samples of a fluorescent labeled assay. Radiationemitted by source 24.4 is imaged by pre-encoder optic 36A.4 to formtarget image 52.4 (an extended image) substantially along a radial axisof modulator 22.4. Target image 52.4 comprises the sub-images of thecollection of different fluorescent samples focused at substantiallydifferent points along said radial axis of modulator 22.4. Modulator22.4 includes a number of radiation filters which encode the radiationemitted by the fluorescent samples to provide an encoded beam comprisinga plurality of encoded spatial components as modulator 22.4 is rotatedabout rotation axis 40. Preferably, target image 52.4 is aligned withthe radiation filters such that the encoded components have asubstantially one to one correspondence with the different fluorescentsamples. In other words, pre-encoder optic 36A.4 images each of thedifferent fluorescent samples to a corresponding sub-image of the targetimage 52.4 on modulator 22.4, where the sub-images preferably do notoverlap on the modulator. The sub-images are preferably dispersed alonga radial axis of the modulator 22.4 such that each encoded spectralcomponent (or a group of encoded spectral components within a bandwidth)from a corresponding sub-image corresponds to one and only one of thedifferent fluorescent samples.

The encoded beam is collected, directed and focused by post-encoderoptic 36B.4 onto detector 26.4, a photo-multiplier tube (PMT), and thesignals generated by the PMT in response to the encoded beam areanalyzed by computer 28.4 to determine the amplitudes of the encodedcomponents. Preferably, the spectral properties of the differentfluorescent samples are measured by inserting a spectrometer or otherwavelength filtering device between post-encoder optic 36B.4 and the PMTand scanning or varying the wavelength of the radiation transmitted tothe PMT. More preferably, a spectrograph or other wavelength separatingdevice is used to direct a number of selected spectral components of theencoded beam to an equal number of PMTs. Most preferably, computer 28.4would include a sufficient number of analog-to-digital converters (ADCs)such that the signals generated by the PMTs in response to the encodedbeam could be analyzed substantially simultaneously. In this manner, thespectral properties of the collection of fluorescent samples can bemeasured substantially simultaneously with the speed and sensitivity ofa PMT.

If necessary, analyzer 100.4 can be combined with the interlacedexcitation mechanism of analyzer 300 (described in FIG. 10) to determinethe excitation properties (e.g., the excitation spectrum) of thedifferent fluorescent samples substantially simultaneously.

The field of view of a given sample is governed by the superposition ofall optical ray traces which begin at the sample (in a correspondingsample plane, comprising part of source 24.4), reflect from the activearea of the corresponding radiation filter, and reach detector(s) 26.4.As a consequence, the field of view changes as the pattern of theradiation filter within the active area changes as modulator 22.4rotates. For non-homogeneous samples, or samples with abrupt boundaries,rotation-dependent variations in the field of view can lead to awaveform distortion of an encoded response component. In the presentinvention, these effects can be minimized by reducing the number ofabrupt discontinuities along one or more axes in the pattern of theradiation filters. Preferably, the radiation filters of modulator 22.4comprise the “bar-code” or “checker-board” like patterns described aboveto provide one or more encoded components with a substantially constantfield of view along one or more axes in the sample plane.

In reference to FIG. 9A. for the analyzer 100.4 described above, theposition of the imaged fluorescence can be controlled by moving one ormore optical elements to align target image 52.4 onto modulator 22.4.Preferably, source 24.4 includes a number of alignment spatialcomponents (e.g., a number of known fluorescent species distributed atknown spatial positions within 24.4) and modulator 22.4 includes anumber of alignment channels to provide input to the alignmentcalibration algorithm 28.utl(ACA).4, which in turn, generates one ormore control signals to position one or more optical elements to aligntarget image 52.4 onto modulator 22. More preferably, the alignmentspatial components would also have known spectral emission propertiesfor calibrating the wavelength filtering device or the wavelengthseparating device.

Example 5

The fifth example of the multi-purpose analyzer 100 depicted in FIG. 1A,analyzer 100.5, is a spectrum analyzer which encodes both a dispersedimage having a plurality of selected spectral components and an extendedimage comprising the radiation transmitted through or reflected from oneor more bandpass filters and/or dichroic beam splitters. This approachmay be useful in situations where the radiation path through theanalyzer may contain interfering gasses and vapors (or liquids) whichcan unpredictably affect the accuracy of the spectral measurements. Insuch instances it is preferable to minimize the optical path through theanalyzer for those spectral components which are subject to theinterference. Carbon dioxide (CO₂) is a well know case in point.Dispersive instruments used in applications where high transmissionaccuracy is desired in the CO₂ spectral region typically include anitrogen purge of the instruments uncontrolled path, i.e., the opticalpath not including the sample or sample cell. Analyzer 100.5 presents analternative to this approach.

In Analyzer 100.5, the radiation source is a broad-band ormulti-wavelength source having plurality of selected spectral componentsin two distinct spectral regions SR1 and SR2. SR1 contains thosespectral components which are subject to the interference in theuncontrolled path. Preferably, analyzer 100.5 includes a dichroic mirrorand one or more bandpass filters or a linear-variable filter (LVF) tofilter the radiation in SR1. Taken together, the radiation source, thedichroic mirror, and the collection of bandpass filters or LVF comprisesource 24.5, having a number of spatial components corresponding to theradiation transmitted through (or reflected from) the individualbandpass filters or positions along the LVF. The radiation in SR2, whichis not subject to the interference, is designated source 24.5.2.Pre-encoder optics, 36A.5 includes sub-optics, 36A.5.1 and 36A.5.2, forindependently imaging 24.5.1 and 24.5.2, respectively, onto modulator22.5. Sub-optic, 36A.5.1 forms a first target image 52.5.1,substantially along a first radial axis of modulator 22.5, and sub-optic36A.5.2, which includes a diffractive or refractive element, forms asecond target image 52.5.2, substantially along a second radial axis ofmodulator 22.5. Target image 52.5.1 comprises selected spectralcomponents of 24.5.1 focused at substantially different points along thefirst radial axis of modulator 22.5. Target image 52.5.2, a dispersedimage, comprises selected spectral components of 24.5.2 focused atsubstantially different points along the second radial axis of modulator22.5.

Modulator 22.5 has a number of radiation filters at different radii forencoding the radiation components of 24.5.1 and 24.5.2 to provide twoencoded beams (56.5.1 and 56.5.2, respectively) as modulator 22.5 isrotated about the rotation axis 40. Preferably, target image 52.5.1 isaligned with the radiation filters such that the encoded components of56.5.1 have a substantially one to one correspondence with the selectedspectral components of 24.5.1. Preferably, target image 52.5.1 isaligned with the radiation filters such that the encoded components of56.5.2 have a substantially one to one correspondence with the selectedspectral components of 24.5.2. Post-encoder optics, 36B.5 includessub-optics, 36B.5.1 and 36B.5.2, for manipulating 56.5.1 and 56.5.2,respectively. 56.5.1 is collected, directed and focused with 36B.5.1onto a first detector 26.5.1, and 56.5.2 is collected, directed andfocused with 36B.5.2 onto a second detector 26.5.2. Preferably, computer28.5 includes two ADCs for sampling the signals from detectors 26.5.1and 26.5.2. Computer 28.5 then analyzes the signals generated bydetector 26.5.1 and detector 26.5.2 in response to encoded beams, 56.5.1and 56.5.2, respectively to determine the amplitudes of the encodedcomponents in both spectral ranges. A sample or sample cell (e.g.,sample 38 shown as a dashed line box in FIG. 1A FIG. 1A) can be insertedbetween the radiation source and the dichroic mirror for spectralanalysis; i.e., the sample is within the confines of source 24.5.Preferably, the total uncontrolled path for the spectral components ofSR1 is made as small as possible to minimize the interference. In thismanner, the spectral properties of a sample can be measured in thepresence of interfering gasses or vapors.

Example 6

The sixth example of the multi-purpose analyzer 100 depicted in FIG. 1A,analyzer 100.6, is compact spectrum analyzer that uses a collection ofdiscrete radiation sources to provide a multi-spectral-component encodedsource for analyzing a sample. Examples of discrete sources includelaser diodes, light-emitting diodes or lamp/filter combinations.Preferably, radiation source 24.6 comprises a linear array of discretesources. The radiation emitted by the array of sources is imaged to formtarget image 52.6 substantially along a radial axis of modulator 22.6.Preferably, the array of sources is positioned close to and along theradius of modulator 22.6 such that target image 52.6 is formed withoutneeding pre-encoder optic 36A. Target image 52.6 comprises spatialcomponents, the sub-images of the radiation emitted by the individualsources, which are focused (or centered) at substantially differentpoints along said radial axis of modulator 22.6. Modulator 22.6 has anumber of radiation filters at different radii for encoding the spatialcomponents to provide an encoded beam as modulator 22.6 is rotated aboutthe rotation axis 40.6. Preferably, the spatial components are alignedwith the radiation filters such that the encoded components have asubstantially one to one correspondence with the radiation emitted bythe individual discrete sources. The encoded beam is collected, directedand focused with post-encoder optic 36B.6 onto detector 26.6. Computer28.6 then analyzes the signal generated by detector 26.6 in response tothe encoded beam to determine the amplitudes of the encoded components.A sample or sample cell can be inserted between the source 24.6 anddetector 26.6. In this manner, the spectral properties of a sample canbe measured.

In reference to FIG. 9A. for analyzer 100.6 described above, theposition of the array of discrete sources, and/or other opticalelements, can be controlled to align target image 52.6 onto modulator22.6. Preferably, source 24.6 includes a number of alignment spatialcomponents and modulator 22.6 includes a number of alignment channels toprovide input to the Alignment Calibration Algorithm 28.utl(ACA).6,which in turn, generates one or more control signals for hardware driver28.6.drv to position one or more optical elements (e.g., a commonstructure onto which the array of discrete sources are mounted) to aligntarget image 52.6 onto modulator 22.6.

Example 7

In some applications, it is necessary to measure the intensities of twoor more groups of selected spectral components in two or more distinctspectral regions. For practical reasons, these spectral regions areoften distinguished by the wavelength response characteristics ofvarious radiation detectors. For example, a Mercury Cadmium Telluride(HgCdTe or MCT) responds to radiation roughly between 8 and 12 microns,a Lead Selenide (PbSe) detector responds to radiation roughly between 3and 5 microns, a Lead Sulfide (PbS) detector responds to radiationroughly between 1 and 3 microns, an Indium Gallium Arsenide (InGaAs)detector responds to radiation roughly between 0.7 and 2.2 microns, anda photo-multiplier tube (PMT) responds to radiation roughly between 0.2and 0.7 microns. In a given applications it may be necessary to measureselected spectral components in various combinations of thesedetector-specific spectral regions.

The seventh example of the multi-purpose analyzer 100 depicted in FIG.1A, analyzer 100.7, is a spectrum analyzer which uses a modulator 22.7with one or more radiation filters which simultaneously encode selectedspectral components in two distinct spectral regions. Radiation source24.7 comprises selected spectral components in two distinct spectralregions, SR1 and SR2. Pre-encoder optic 36A.7 collects the radiationemitted by radiation source 24.7 and forms two target images, 52.7.1 and52.7.2. In one embodiment, pre-encoder optic 36A.7 may contain one ormore gratings having two or more distinct grove frequencies. In thismanner, the multi-groove-frequency grating would disperse two distinctspectral regions substantially along the same optical path (i.e.,dispersed images 52.7.1 and 52.7.2 would overlap one another). Targetimage 52.7.1 comprises selected spectral components from SR1, and targetimage 52.7.2 comprises selected spectral components from SR2. Theselected spectral components of 52.7.1 are focused at substantiallydifferent points along a radial axis of modulator 22.7. Similarly, theselected spectral components of 52.7.2 are focused at substantiallydifferent points along a radial axis of modulator 22.7. If required,pre-encoder optic 36A can be engineered such that 52.7.1 and 52.7.2 areseparated along the radial axis, or projected along two different radialaxes. Such and other variations are within the scope of the invention.Modulator 22.7 has a number of radiation filters at different radii forencoding the spectral components to provide two coinciding encodedbeams, 56.7.1 and 56.7.2, as modulator 22.7 is rotated about therotation axis 40. Preferably, target images 52.7.1 and 52.7.2 arealigned with the radiation filters such that the encoded components havea substantially one to one correspondence with the selected spectralcomponents of SR1 and SR2. More preferably, modulator 22.7 is an“array-like” pattern comprising a large number of substantiallyorthogonal radiation filters substantially adjacent to one another,forming a substantially gapless encoding grid to simultaneously probeboth spectral ranges of radiation source 24.7. Most preferably, theindividual widths of the radiation filters in modulator 22.7 areengineered to provide encoded spectral components with constantwavelength bandwidth or constant energy bandwidth in a given spectralrange. Using the “array-like” pattern of modulator 22.7, 56.7.1 and56.7.2 contain substantially complete spectra in spectral ranges SR1 andSR2, respectively. Encoded beams 56.7.1 and 56.7.2 are collected,separated and focused with post-encoder optic 36B.7 onto detectors26.7.1 and 26.7.2, respectively; e.g. using one or more dichroicmirrors. Preferably, detector 26.7.1 responds to the selected spectralcomponents or SR1 and detector 26.7.2 responds to the selected spectralcomponents or SR2. Preferably, computer 28.7 has two ADCs for samplingthe signals from detectors 26.7.1 and 26.7.2 substantiallysimultaneously. Computer 28 then analyzes the signal generated by thetwo detectors in response to the two encoded beams to determine theamplitudes of selected encoded components in the two spectral rangessubstantially simultaneously. A sample or sample cell can be insertedbetween the source 24.7 and modulator 22.7. In this manner, the spectralproperties of a sample in two distinct spectral ranges can be measuredsimultaneously.

The spectral regions cited in the example above where chosen for clarityand are not meant to limit the scope of the invention.

Example 8

The eighth example of the multi-purpose analyzer 100 depicted in FIG.1A, analyzer 100.8, is a multi-spectral-component encoded source with ahigh-intensity, collimated beam which can be used to excite radiationemitting or radiation scattering samples (e.g., gas clouds, contaminatedwater, contaminated surfaces, contaminated soils). Radiation source 24.8is a collimated radiation beam having a plurality of selected excitationcomponents (e.g., an argon-ion or other multi-excitation-line laser, ormultiple independent excitation sources). Pre-encoder optic 36A.8includes at least one diffractive or refractive element to separate theselected spectral components to form target image 52.8 along a radialaxis of modulator 22.8. Preferably, pre-encoder optic 36A.8 includes avariable attenuator to precondition or preset the intensities of theselected components. Target image 52.8 is a dispersed image comprisingselected spectral components focused at substantially different pointsalong one or more radial axes of modulator 22.8. Modulator 22.8 includesa number of radiation filters which encode the selected spectralcomponents to provide an encoded beam comprising a plurality of encodedspectral components as modulator 22.8 is rotated about rotation axis 40.Preferably, target image 52.8 is aligned with the radiation filters suchthat the encoded components have a substantially one to onecorrespondence with the selected spectral components. Preferably, afirst post-encoder optic 36B.8.1 includes at least one diffractive orrefractive element to substantially re-collimate the encoded components(e.g., 36A.8 and 36B.8.1 each comprises at least one grating pair, prismpair or prism-grating combination). In this manner, the encoded beam canbe propagated over a distance to excite a remote sample 38 (e.g., a gascloud or contaminated surfaces), or excite one or more optically densesamples (e.g., contaminated surfaces, contaminated water, andcontaminated soils). The sample 38 (shown as a dashed line box in FIG.1A) may or may not be confined in an enclosure.

In response to the encoded excitation beam, the sample 38 emits encodedresponse radiation, which is collected and directed by a secondpost-encoder optic 36B.8.2 (e.g., a telescope for remote samples, or amicroscope for optically dense samples, not shown in FIG. 1A) back todetector 26.8. Computer 28.8 analyzes the signal generated by detector26.8 in response to the encoded response beam to determine amplitudes ofthe encoded components. In this manner, the excitation properties of thesample can be used as input to one or more Chemometric analyses todetermine the chemical composition of the sample; e.g., to detectflammable or toxic chemicals, including chemical or biochemical weapons.

In another embodiment of analyzer 100.8, the collimated, encoded beam islaunched into an optical fiber, waveguide, light pipe or purged (orevacuated) tubing and distributed to one or more remote samplingstations such that the uncontrolled path of the encoded excitation beamis substantially limited outside of the remote sampling station. Theremote sampling station includes one or more remote samples that emit orscatter encoded response radiation in response to the encoded excitationbeam. Preferably, each of the remote excitation stations includes atleast one remote detector RD26 and a remote computer RC28 (with the samedecoding functionality as computer 28) for analyzing the encodedresponse radiation. Preferably, the timing and alignment signals aredispatched to the remote sampling stations for use by RD28 to analyzethe signals from RD26. In this manner, the data acquired at the remotelocations can be properly analyzed.

Preferably, pre-encoder optic 36A.8 and post-encoder optic 36B.8.1 canbe substantially simplified by engineering source 24.8 to provideselected components spatially separated from one another (e.g., spatialvariations in the gain medium or replace the partial mirror of a laserwith a patterned array of dichroic mirrors). More preferably, source24.8 is engineered to provide selected components at spatial locationsthat substantially match the pattern of radiation filters and filterpairs on modulator 22.8.

In reference to FIG. 9A. for the analyzer described above, the positionof one or more optical element can be controlled to align target image52.8 onto modulator 22.8. Preferably, modulator 22.8 includes one ormore alignment radiation filters or filter pairs to encode one or morealignment components of source 24.8. The alignment components provideinput to the Alignment Calibration Algorithm 28.utl(ACA).8, which inturn, generates one or more control signals to position one or moreoptical elements to properly align target image 52.8 onto modulator22.8.

Example 9

The ninth example of the multi-purpose analyzer 100 depicted in FIG. 1A,analyzer 100.9, is an imaging analyzer which uses one or more radiationexcitation sources and imaging optics (e.g., optics designed to providea line image or multiple sub-images for each excitation source) toprovide an array of encoded excitation beams (each excitation beamhaving substantially constant spot size and substantially uniformillumination along one or more axes) for exciting a collection ofsamples. Examples of excitation sources include gas lasers, glasslasers, laser diodes, light-emitting diodes and lamp/filtercombinations. Examples of collections of samples include an array of gasor liquid sample cells, a multi-lane electrophoresis, the wells or blotsof a fluorescent labeled assay, regions in a non-homogeneous mixture,and pharmaceuticals on an assembly line. The radiation emitted byradiation excitation source 24.9 is imaged with pre-encoder optic 36A.9to form target image 52.9 substantially along a radial axis of modulator22.9. Target image 52.9 comprises an array of sub-images (or a lineimage, which is a continuum of sub-images) of radiation source 24.9,which are focused (or centered) at substantially different points alongsaid radial axis of modulator 22.9. Modulator 22.9 has a number ofradiation filters at different radii for encoding the sub-images toprovide an array of encoded excitation beams as modulator 22.9 isrotated about rotation axis 40. Preferably, the sub-images are alignedwith the radiation filters such that the encoded excitation beams have asubstantially one to one correspondence with the radiation comprisingthe individual sub-images. The encoded excitation beams are collected,directed and focused with post-encoder optic 36B.9.1 onto a collectionof samples. If more than one excitation source is used, analyzer 100.9can be combined with Excitation Interlacing Optic (described above) toprovide a unique encoding for each sample/excitation combination.Preferably, the array of encoded excitation beams is aligned with thecollection of samples such that each sample is excited with one encodedexcitation beam from each excitation source.

In response to the excitation radiation, each said sample emits orscatters one or more response beams of radiation. Preferably, the arrayof encoded excitation beams is aligned with the collection of samplessuch that a substantially one-to-one correspondence exists between agiven encoded response component and a given sample/excitationcombination (i.e., each sample emits or scatters one encoded responsebeam for each excitation source. Excitation cross-talk, resulting froman encoded excitation beam exciting more than one sample, is to beavoided.). The encoded response beams are collected, directed, andfocused by post-encoded optic 36B.9.2 onto detector 26.9, aphoto-multiplier tube (PMT), and the signals generated by the PMT inresponse to the encoded beam are analyzed by computer 28.9 to determinethe amplitudes of the encoded components.

Preferably, the spectral properties of the different fluorescent samplesare measured by inserting a spectrometer or other wavelength filteringdevice between post-encoder optic 36B.9 and the PMT and scanning thewavelength of the radiation transmitted to the PMT. More preferably, aspectrograph or other wavelength separating device is used to direct anumber of selected spectral components of the encoded beam to an equalnumber of PMTs. Most preferably, computer 28.9 would include asufficient number of analog-to-digital converters (ADCs) such that thesignals generated by the PMTs in response to the encoded beam could beanalyzed substantially simultaneously. In this manner, the spectralproperties of the response of a collection of samples to one or moresources of excitation radiation can be measured substantiallysimultaneously with the speed and sensitivity of a PMT.

The field of illumination in a given sample plane is governed by thesuperposition of excitation ray traces which begin at source 24.9,reflect from the active area of the corresponding radiation filter, andreach the corresponding sample. As a consequence, the field ofillumination (on the sample, in the sample plane) changes as the patternof the radiation filter within the active area changes as modulator 22.9rotates. For non-homogeneous samples, or samples with abrupt boundaries,rotation-dependent variations in the field of illumination can lead to awaveform distortion of an encoded response component. In the presentinvention, these effects can be minimized by reducing the number ofabrupt discontinuities along one or more axes in the pattern of theradiation filters. Preferably, at least one of the radiation filters ofmodulator 22.9 comprises the “bar-code” or “checker-board” like patternsdescribed above to provide one or more encoded excitation componentswith a substantially constant field of illumination along one or moreaxes in the sample plane.

In reference to FIG. 9A. for analyzer 100.9 described above, theposition of the array of excitation sub-images, the position of thearray of encoded excitation beams, the position of the ample collection,and/or other optical elements, can be controlled to align target image52.9 onto modulator 22, and align the encoded excitation beams onto thesample collection. Preferably, source 24.9 includes a number ofalignment spatial components and modulator 22 includes a number ofalignment channels to provide input to the alignment calibrationalgorithm 28.utl(ACA).9, which in turn, generates one or more controlsignals to position one or more optical elements (e.g., a commonstructure onto which the array of discrete sources are mounted analogousto 35.FP shown in FIG. 17A) to align target image 52.9 onto modulator22.

Example 10

The tenth example of the multi-purpose analyzer 100 depicted in FIG. 1A,analyzer 100.10, is a multi-spectral-component encoded source with ahigh-intensity, collimated beam which is used to probe optically densesamples such as liquids or solids (e.g., drinking water,pharmaceuticals, walls, contaminated soils, and luggage and packages ona baggage conveyer). The sample 38 may be placed at any point in theoptical path between source 24.10 and the detector 26.10, such as in thelocation shown in FIG. 1A, except that the beam from the source may bescattered by the sample instead of passing through it, and the scatteredradiation conveyed to the detector. Radiation source 24.10 is acollimated radiation beam having a plurality of selected spectralcomponents (e.g., a carbon dioxide laser, an argon ion laser, or othermulti-line laser). Pre-encoder optic 36A.10 includes at least onediffractive or refractive element to separate the selected spectralcomponents to form target image 52.10 along a radial axis of modulator22.10. Preferably, pre-encoder optic 36A.10 includes a variableattenuator to precondition or preset the intensities of the selectedcomponents. Target image 52.10 is a dispersed image comprising selectedspectral components focused at substantially different points along oneor more radial axes of modulator 22.10. Modulator 22.10 includes anumber of radiation filters which encode the selected spectralcomponents to provide an encoded beam comprising a plurality of encodedspectral components as modulator 22.10 is rotated about rotation axis40. Preferably, target image 52.10 is aligned with the radiation filterssuch that the encoded components have a substantially one to onecorrespondence with the selected spectral components. Preferably, afirst post-encoder optic 36B.10.1 includes at least one diffractive orrefractive element to substantially re-collimate the encoded components(e.g., 36A.10 and 36B.10.1 each comprises at least one grating pair,prism pair or prism-grating combination). In this manner, the encodedbeam can be used to probe optically-dense samples. A second post-encoderoptic 36B.10.2 collects the encoded radiation beam and directs it backto detector 26.10. Preferably, a sample (e.g., sample 38 shown as adashed line box in FIG. 1A) is placed between post-encoder optic36B1.10.1 and post-encoder optic 36B1.10.2. Computer 28.10 analyzessignal 27.10 generated by detector 26.10 in response to encoded beam56.10 to determine amplitudes of the encoded components. In this manner,the spectral transmission of the optically-dense sample can be used asinput to a Chemometric analysis to provide a chemical compositionanalysis of the sample; e.g., to detect flammable or toxic chemicals,including chemical or biochemical weapons.

In a related embodiment of analyzer 100.10, the encoded beam ispropagated over a long distance to at least one remote detector RD26(similar to detector 26.10, but located at a remote location).Preferably, the signals generated by RD26 in response to the encodedbeam are sent back to analyzer 100.10 for analysis by computer 28.10,which determines the amplitudes of the encoded components. Morepreferably, remote detector RD26 is augmented by a remote computer RC28to comprise a remote receiver, and the timing and alignment signals aredispatched (e.g., via microwave signal, fiber optic or one or moreadditional encoded laser beams) to the remote receiver such that thedetector signal can be analyzed at the remote location by RC28. Mostpreferably, the encoded beam is split up with a beam splitter anddistributed along with the timing and alignment signals to a number ofremote receivers. In this manner, the detector signals can be analyzedat each of the remote locations.

In another embodiment of analyzer 100.10, the collimated, encoded beamis launched into an optical fiber, waveguide, light pipe or purged (orevacuated) tubing and distributed to one or more remote samplingstations such that the uncontrolled path of the encoded beam issubstantially limited outside of the remote sampling station.Preferably, each of the remote sampling stations include at least oneremote detector RD26 and a remote computer RC28 (with the same decodingfunctionality as computer 28) for analyzing the signals generated by thedetector and the timing and alignment signals. In this manner, the dataacquired at the remote locations can be properly analyzed.

Preferably, pre-encoder optic 36A.10 and post-encoder optic 36B.10.1 canbe substantially simplified by engineering source 24.10 to provideselected components spatially separated from one another (e.g., spatialvariations in the gain medium or replace the partial mirror of a laserwith a patterned array of dichroic mirrors). More preferably, source24.10 is engineered to provide selected components at spatial locationsthat substantially match the pattern of radiation filters and filterpairs on modulator 22.10.

In reference to FIG. 9A. for the analyzer described above, the positionof one or more optical element can be controlled to align target image52.10 onto modulator 22.10. Preferably, modulator 22.10 includes one ormore alignment radiation filters or filter pairs to encode one or morealignment components of source 24.10. The alignment components provideinput to the Alignment Calibration Algorithm 28.utl(ACA).10, which inturn, generates one or more control signals to position one or moreoptical elements to properly align target image 52.10 onto modulator22.10.

Example 11

The eleventh example of the multi-purpose analyzer 100 depicted in FIG.1A, analyzer 100.11, is a spectrum analyzer employing radiation filtersand radiation filter pairs to identify and quantify (different,labeling, distinct, signatures) various fluorescence spectra from anumber of dye-labeled beads dispersed in a fluid.

In Analyzer 100.11, radiation source 24.11 is superposition offluorescence from a number of dye-labeled beads dispersed in a fluid.Pre-encoder optics, 36A.11, which includes a diffractive or refractiveelement, forms a dispersed target image 52.11, substantially along aradial axis of modulator 22.11. Modulator 22.11 has a number ofradiation filters at different radii for encoding the selected radiationcomponents of 24.11.1 to provide an encoded beam as modulator 22.11 isrotated about the rotation axis 40.11. Preferably, target image 52.11 isaligned with the radiation filters such that the encoded components havea substantially one-to-one correspondence with the selected spectralcomponents of 24.11. Post-encoder optics, 36B.11, collects, directs andfocuses the encoded beam onto detector 26.11. Computer 28.11 includes anADC for sampling the signals from detector 26.11. Computer 28.11 thenanalyzes the signals generated by detector 26.11 in response to encodedbeams to determine the amplitudes of the encoded components. Computer28.11 subsequently uses the decoded amplitudes in one or moreChemometric algorithms to determine the presence and intensity offluorescence from one or more labeling dyes. In this manner, thepresence and concentration of one or more chemicals (or biochemicals)that alter the intensity of one or more labeling dyes (e.g., by enablingor disabling one or more fluorescence quenching mechanisms) can bedetermined.

Preferably, modulator pattern 21.11 includes one or more complementaryfilter pairs to enable computer 28.11 to employ Chemometric algorithmsusing one or more wavelength-first-derivative basis functions todiscriminate between fluorescence from two or more labeling dyes havingsimilar fluorescence spectra, by means such as by determining thezero-crossings of the spectra, which may be different for differentlabeling dyes, even though they have similar fluorescence spectra. Morepreferably, modulator pattern 21.11 includes one or more complementaryfilter pairs and one or more filters (or collect filter pairs),occupying annular segments within the same annular region (e.g.,patterns similar to those of modulator 22E of FIG. 8), to enablecomputer 28.11 to simultaneously discriminate and quantify fluorescencefrom two or more labeling dyes having similar fluorescence spectra.

Example 12

The twelfth example of the multi-purpose analyzer 100 depicted in FIG.1A, analyzer 100.12, is a multi-spectral-component encoded source with ahigh-intensity, collimated beam that can be used to identify andquantify gasses, vapors and particulates contained within one or moreenclosed paths based on analyses of absorption, scattering orfluorescence. Examples of enclosed paths include the ductwork of an HVACsystem, the tank of a tanker truck or railcar, a gas pipeline (e.g.,natural gas), the hold of a container ship, cargo containers, and subwaytunnels.

Radiation source 24.12 is a collimated radiation beam having a pluralityof selected spectral components (e.g., a carbon dioxide laser, anargon-ion laser, or other multi-line laser). Pre-encoder optic 36A.12includes at least one diffractive or refractive element to separate theselected spectral components to form a target image along a radial axisof modulator 22.12. Preferably, pre-encoder optic 36A.12 includes avariable attenuator to precondition or preset the intensities of theselected components. Target image 52.12 is a dispersed image comprisingselected spectral components focused at substantially different pointsalong said radial axis of modulator 22.12. Modulator 22.12 includes anumber of radiation filters which encode the selected spectralcomponents to provide an encoded beam comprising a plurality of encodedspectral components as modulator 22.12 is rotated about rotation axis40. Preferably, target image 52.12 is aligned with the radiation filterssuch that the encoded components have a substantially one to onecorrespondence with the selected spectral components. Preferably, afirst post-encoder optic 36B.12.1 includes at least one diffractive orrefractive element to substantially re-collimate the encoded components(e.g., 36A.12 and 36B.12.1 each comprises at least one grating pair,prism pair or prism-grating combination). In this manner, the encodedbeam can be propagated through a long, enclosed path to a remotereflector and directed back to detector 26.12. Examples of remotereflectors include a retro-reflector, a simple mirror, metallicductwork, or various target objects providing diffuse or specularreflectance. A second post-encoder optic 36B.12.2 collects the encodedradiation beam and directs it back to detector 26.12. Computer 28.12decodes signal 27.12 generated by detector 26.12 to determine amplitudesof the encoded components, which are subsequently used as inputs for oneor more Chemometric analyses. In this manner, the chemical compositionof the closed path can be determined. This information can then be usedto alert to the presence of specific gasses and vapors; e.g., flammableor toxic chemicals, including chemical and biochemical weapons.

In one embodiment, the containers of a container ship can be equippedwith optical windows such that the internal air space can be probed.More preferably, the location of the optical windows is standardizedsuch that the closed path comprises the sum of the internal air spacesof at least two containers positioned side-by-side or end-to-end in thecargo hold. More preferably, the containers are equipped with samplecell 38.12 (cell 38 shown as a dashed line box in FIG. 1A), which spansthe internal volume between the standardized optical windows. Morepreferably, the sample cells are equipped with absorbing media 37.12.More preferably, the sample cells are equipped with heating mechanism39.12 (mechanism 39 shown as a dashed line box in FIG. 1A) to desorbchemical trapped by the adsorbing media. Most preferably, absorbingmedia 37.12 is heated by a laser or other wireless means to desorb theadsorbed chemical. In this manner, a large number of containers can beefficiently probed for toxic chemicals and contraband prior to enteringport.

In a related embodiment of analyzer 100.12, the encoded beam ispropagated through a closed path to at least one remote detector,RD26.12, (similar to detector 26, but located at a remote location).Preferably, the signals generated by RD26 in response to the encodedbeam are sent back to analyzer 100.12 for analysis by computer 28.12,which determines the amplitudes of the encoded components. Morepreferably, remote detector RD26.12 is combined with remote computerRC28.12 to comprise a remote receiver, and the timing and alignmentsignals are dispatched to the remote receiver such that the detectorsignal can be analyzed at the remote location by RC28. Most preferably,the encoded beam is split up with a beam splitter and distributed alongwith the timing and alignment signals to a number of remote receivers;e.g., distributed throughout an HVAC system, pipeline network, or thehold of a container vessel. In this manner, the detector signals can beanalyzed at each of the remote locations, and a number of closed pathscan be simultaneously probed for the presence and concentration ofgasses, vapors and particulates; e.g., flammable or toxic chemicals,including chemical and biochemical weapons.

Preferably, pre-encoder optic 36A.12 and post-encoder optic 36B.12.1 canbe substantially simplified by engineering source 24.12 to provideselected components spatially separated from one another (e.g., spatialvariations in the gain medium or replace the partial mirror of a laserwith a patterned array of dichroic mirrors). More preferably, source24.12 is engineered to provide selected components at spatial locationsthat substantially match the pattern of radiation filters and filterpairs on modulator 22.12.

If source 24.12 has an emission repetition rate that is comparable to orless than the data acquisition rate, it is preferred that the rotationof modulator 22.12 be synchronized with the repetition rate to minimizealiasing effects on the decoded amplitudes.

In reference to FIG. 9A. for the analyzer described above, the positionof one or more optical element can be controlled to align target image52.12 onto modulator 22.12. Preferably, modulator 22.12 includes one ormore radiation filters or filter pairs to encode one or more spectralcomponents in source 24.12 to provide input to the alignment calibrationalgorithm 28.utl(ACA).12, which in turn, generates one or more controlsignals to position one or more optical elements to properly aligntarget image 52.12 onto modulator 22.12.

Example 13

The thirteenth example of the multi-purpose analyzer 100 depicted inFIG. 1A, analyzer 100.13, is a multi-spectral-component encoded sourcewith a collimated beam that is combined with non-encoded radiation beamto provide a heat source, which is used to identify and quantify gassesand vapors desorbed from a surface (or absorbing media 37.13, with 37shown in dashed line box in FIG. 1A) by a heat source 39.13 (heatingmechanism 39 shown as a dashed line box in FIG. 1A), or produced in aplasma initiated by the heat source (e.g., spectral analysis of a lasercutting torch). The desorbed material then form a sample 38.13 that isprobed by analyzer 100.13 as described below.

Radiation source 24.13 is a high-energy collimated radiation beam havinga plurality of selected spectral components (e.g., a carbon dioxidelaser). Radiation source 24.13 includes a beam splitter (not shown inFIG. 1A) to separate the collimated radiation beam to provide two ormore radiation beams having substantially different intensities and/orpowers. The first beam 24.13.1 comprises selected spectral componentshaving intensities substantially appropriate for spectral analysis. Thesecond beam 24.13.2 comprises radiation having intensities substantiallyappropriate for desorbing chemicals from a sample surface or initiatinga plasma.

Pre-encoder optic 36A.13 includes at least one diffractive or refractiveelement to separate the selected spectral components from 24.13.1 toform a target image along a radial axis of modulator 22.13. Target image52.13 is a dispersed image comprising selected spectral componentsfocused at substantially different points along said radial axis ofmodulator 22.13. Modulator 22.13 includes a number of radiation filterswhich encode the selected spectral components to provide an encoded beamcomprising a plurality of encoded spectral components as modulator 22.13is rotated about rotation axis 40. Preferably, target image 52.13 isaligned with the radiation filters such that the encoded components havea substantially one to one correspondence with the selected spectralcomponents. Preferably, a first post-encoder optic 36B.13.1 includes atleast one diffractive or refractive element to substantiallyre-collimate the encoded components (e.g., 36A.13 and 36B.13.1 compriseat least one grating pair, prism pair or prism-grating combination).Radiation beam 24.13.2 is used to desorb chemicals adsorbed on a samplesurface. The desorbed chemicals are subsequently probed with the encodedradiation beam (originating from 24.13.1). A second post-encoder optic36B.13.2 collects the encoded radiation beam and directs it back todetector 26.13. Computer 28.13 decodes signal 27.13 generated bydetector 26.13 to determine amplitudes of the encoded components, whichare subsequently used as inputs for one or more Chemometric analyses. Inthis manner, the chemical composition of the containers can bedetermined. This information can then be used to alert to the presenceof specific gasses and vapors; e.g., flammable or toxic chemicals,including chemical and biochemical weapons.

In one application, cargo containers (e.g., from a container ship,train, airplane, or truck) can be equipped with a sample cell accessiblethrough one or more optical windows. The sample cell comprises a fixedpath, a mirror and an adsorbing media. Preferably, the adsorbing mediais exposed to the internal atmosphere of the container for the durationof the voyage to maximize the probability that one or more targetchemicals (e.g., chemical weapons, contraband, etc . . . ) are absorbedin sufficient quantity for detection. Radiation beam 24.13.2 is used toheat the adsorbing media, and encoded radiation beam 24.13.1 is used toprobe the contents of the sample cell 38.13. Preferably, the sample isscanned for flammable gasses prior to heating to minimize the risk ofexplosion. In this manner, a large number of containers can be safelyand efficiently probed for toxic chemicals and contraband.

Preferably, pre-encoder optic 36A.13 and post-encoder optic 36B.13.1 canbe substantially simplified by engineering source 24.13 to provideselected components spatially separated from one another (e.g., spatialvariations in the gain medium or replace the partial mirror of a laserwith a patterned array of dichroic mirrors). More preferably, source24.13 is engineered to provide selected components at spatial locationsthat substantially match the pattern of radiation filters and filterpairs on modulator 22.13.

In reference to FIG. 9A. for the analyzer described above, the positionof one or more optical element can be controlled to align target image52.13 onto modulator 22.13. Preferably, modulator 22.13 includes one ormore alignment radiation filters or filter pairs to encode one or morealignment components of source 24.13. The encoded alignment componentsare analyzed to provide input to the alignment calibration algorithm28.utl(ACA).13, which in turn, generates one or more control signals toposition one or more optical elements to properly align target image52.13 onto modulator 22.13.

Example HS.1

The next example is based on the Hyper-Spectral Imaging Analyzerdescribed above in FIGS. 12A and 12B. Radiation source 24.HS.1 is amulti-lane (or multi-capillary), four-dye-labeled electrophoresis (otherexamples of radiation source 24.HS.1 include a multi-well microtiterplate, or multi-gel-blot microarray) responding to one or morecomponents of excitation radiation. Radiation emitted or scattered bysource 24.HS.1 is imaged by pre-encoder optic 536A.HS.1 to form targetimage 52.HS.1 on modulator 22.HS.1. Target image 52.HS.1 comprises aplurality of dispersed sub-images, corresponding to the excitedelectrophoresis lanes (or capillaries), with their respective dispersionaxes substantially separated from one another (or carefully interlaced)along a common radius of modulator 22.HS.1. Preferably, analyzer100.HS.1 includes a bandpass filter that transmits selected spectralcomponents from each dispersed sub-image, while preventing the dispersedsub-images from interfering with one another. Modulator 22.HS.1 includesa plurality of sub-patterns for encoding the dispersed sub-images. Eachsub-pattern includes a number of radiation filters to encode theselected spectral components as modulator 22.HS.1 is rotated aboutrotation axis 40. Preferably, the selected spectral components aresufficient to determine the individual concentration of each of the fourdyes used in the electrophoresis. Preferably, target image 52.HS.1 isaligned with modulator 22.HS.1 such that the encoded components have asubstantially one to one correspondence with the selected spectralcomponents for each lane (or capillary). In other words, each lane willhave its corresponding encoded component, where the encoded componentsfor different lanes are substantially orthogonal to one another. Theencoded beam comprising all of the encoded components from all the lanesis collected, directed and focused with post-encoder optic 36B.HS.1 ontodetector 26.HS.1, e.g., a photo-multiplier tube (PMT). Computer 28 thenanalyzes the signal generated by detector 26.HS.1 in response to theencoded beam to determine the amplitudes of the encoded components.Since the encoded components corresponding to the different lanes aresubstantially orthogonal to one another, it is possible determine theamplitudes of the encoded components from the output of detector26.HS.1. Application-specific analytical function 28.asf then uses thedecoded amplitudes to determine the individual concentrations of thefour dyes in each of the lanes (or capillaries) as a function of time togenerate a corresponding four-color electropherograms.

If necessary, analyzer 100.HS.1 can be combined with the interlacedexcitation mechanism (described in FIG. 10A) to determine the excitationproperties (e.g., the excitation spectrum) of the differentelectrophoresis lanes (or capillaries). It is typical for each of thefour dyes to have a unique excitation/response spectrum (or matrix). Inthis manner, the selected spectral components can be measured as afunction of the excitation components substantially simultaneously toenhance the instruments specificity to the four dyes.

In reference to FIG. 9A. for analyzer 100.HS.1 described above, it ispreferable that excitation radiation scattered from the individual lanesor capillaries be used as alignment components. Preferably, the bandpassfilter attenuates the intensity of the alignment components such thatthe amplitude of the encoded alignment components are similar to thenominal encoded amplitudes of the selected spectral components.Preferably, each sub-pattern on modulator 22.HS.1 would include one ormore alignment filter pairs centered at the preferred or expectedposition of the alignment component(s) to provide input to the alignmentcalibration algorithm 28.utl(ACA).HS.1. Preferably, 28.utl(ACA).HS.1would compare the alignment signals to one or more calibration curves(generated as described above) to generate calibration coefficientswhich quantify the alignment error for each dispersed image in targetimage 52.HS.1. Application-specific analytical function 28.asf wouldthen use the calibration coefficients to compensate the encodedcomponents for the alignment error. Most preferably, alignmentcalibration algorithm 28.utl(ACA) would generate one or more controlsignals to position one or more optical elements to properly aligntarget image 52.HS.1 onto modulator 22.HS.1.

The number of excitation components, electrophoresis lanes (orcapillaries), and the number of dyes was chosen for illustrativepurposes, it being understood that arbitrary numbers of excitationcomponents, electrophoresis lanes (or capillaries), and dyes are withinthe scope of the invention.

Example FP.1

The next example is based on Encoded Filter-Photometer Analyzerdescribed above in FIGS. 17A and 17B. Analyzer 100.FP.1 uses one or morebroadband radiation sources and an array of correlation cells (i.e.,target and reference cells filled with various gasses or liquids) toprovide an array of encoded correlation beams (comprising target(s) andreference beams) for probing an unknown sample. Examples of target beamsinclude radiation filtered by CO, CO₂, NO_(x), N₂O, H₂O, H₂S and varioushydrocarbons, including the constituents of natural gas. Due to theinherent danger, radiation filtered by chemical weapons and other toxicgasses and liquids make less practical examples of target beams.Examples of reference beams include radiation filtered by N₂, water, asolvent or vacuum. Examples of samples include ambient air, automobileexhaust, a process stream and natural gas. Such and other examples ofsamples, and target and reference beams, are within the scope of theinvention.

In analyzer 100.FP.1, one or more broadband radiation sources arecoupled into the array of target and reference cells (e.g., by using oneor more of the following components: a cylindrical lens, a lens array, adiffractive optic, or by using an array of sources butted into one ormore correlation cells). The radiation transmitted through the array oftarget and reference cells, which comprises extended radiation source24.FP.1, is imaged with pre-encoder optic 36A.FP.1 to form target image52.FP.1 substantially along a radial axis of modulator 22.FP.1. Targetimage 52.FP.1 comprises an array of sub-images corresponding to theradiation transmitted through the target and reference cells ofradiation source 24.FP.1, which are focused (or centered) atsubstantially different points along said radial axis of modulator22.FP.1. Modulator 22.FP.1 has a number of radiation filters atdifferent radii for encoding the sub-images to provide an array ofencoded correlation beams as modulator 22.FP.1 is rotated about rotationaxis 40. Preferably, the sub-images are aligned with the radiationfilters such that the encoded correlation beams have a substantially oneto one correspondence with the radiation transmitted through theindividual target and reference cells (i.e., correlation cells).

The encoded correlation beams are collected, directed and focused withpost-encoder optic 36B.FP.1 through one or more samples (e.g., sample 38shown as a dashed line box in FIG. 1A, a sample cell in a processstream, a sample cell in a pipeline, and an open path ambient airmeasurement).

Preferably, the target and reference cells are interlaced in the mannerillustrated in FIG. 10A such that each target beam is adjacent to acorresponding reference beam, to comprise a target/reference pair havingsubstantially identical paths within the sample cell, and/orsubstantially identical intensity distributions on the surface ofdetector 26.FP.1. More preferably, the target and reference beams of agiven pair are encoded with a complementary filter pair, such that theamplitude and phase of the resulting encoded component are determined bythe relative intensity of the target and reference beams in the mannerillustrated in FIGS. 17A and 17B. Most preferably, the relativemodulation intensity of the complementary filters is engineered (e.g.,by inserting a neutral density filter in the path of the correspondingreference beam, by varying the width or modulation depth of thereference filter with respect to the target filter) to null theresulting encoded component in the absence (or a nominal level) of acorrelating absorption in the sample cell. In this manner, analyzer100.FP.1 provides a correlation radiometry measurement of the highestphotometric accuracy.

Preferably, the spectral range of the target and reference beam pair arelimited (preferably together) by one or more dichroic mirrors orbandpass filters to isolate the dominant spectral features of the targetchemical. In this manner, the sensitivity (e.g., the amplitude of theencoded target/reference pair in response to a given concentration ofthe target chemical in the sample cell) of the instrument to one or moretarget chemicals in the sample cell can be enhanced.

After propagating through the sample cell, the encoded correlation beamsare collected, directed, and focused by post-encoded optic 36B.FP.1.2onto detector 26.FP.1, and the signal generated by 26.FP.1 in responseto the encoded beams is analyzed by computer 28.FP.1 to determine theamplitudes of the encoded components. The amplitudes of the encodedcomponents are subsequently used by application specific algorithm28.FP.1.asf (e.g., correlation radiometry algorithm) to determine thepresence and concentrations of one or more target chemicals in thesample. If one or more sample cell is probed, multiple detectors andADCs can be used as described previously (e.g., see Example 9). In thismanner, multiple samples can be probed substantially simultaneously.

The path of a given encoded beam through the system (including thesample or correlation cell) is actually a superposition of the pathsfrom all optical ray traces which begin at source 24.FP.1, reflect fromthe active area of the corresponding radiation filter on modulator22.FP.1, and reach detector 26.FP.1. As a consequence, the superpositionof paths changes as the pattern of the radiation filter within theactive area changes as modulator 22.FP.1 rotates. In the presence ofabsorbing analytes (samples or targets) where the attenuation of thebeam depends of the path length, the variation in the superposition ofthe paths can lead to a waveform distortion of an encoded component. Inthe present invention, these effects can be minimized by reducing thenumber of abrupt discontinuities along one or more axes in the patternof the radiation filters. Preferably, at least one of the radiationfilters of modulator 22.FP.1 comprises the “bar-code” or “checker-board”like patterns described above to provide one or more encoded componentswith a substantially constant superposition of optical paths through thesystem.

In reference to FIG. 9A. for analyzer 100.FP.1 described above, theposition of the array of correlation sub-images, the position of thearray of target and reference cells, the position of the sample cell(s),and/or other optical elements, can be controlled to align target image52.FP.1 onto modulator 22, and align the encoded correlation beams topass through the sample cell(s) onto the detector. Preferably, source24.FP.1 includes a number of alignment spatial components and modulator22 includes a number of alignment channels to provide input to thealignment calibration algorithm 28.utl(ACA).FP.1, which in turn,generates one or more control signals to position one or more opticalelements (e.g., a common structure onto which the array target andreference cells are mounted) to align target image 52.FP.1 ontomodulator 22.

In the preceding example, the order of the optical elements was chosenfor illustrative purposes and is not intended to limit the scope of theinvention. For example, the position of the target and reference cellarray with respect to the encoder is arbitrary. The radiationtransmitted through the correlation cells can be encoded or theradiation can be encoded and then transmitted through the correlationcells. In addition, the sample (e.g., sample 38 38 shown as a dashedline box in FIG. 1A) can be placed anywhere between source 24.FP.1 anddetector 26.FP.1 in the beam path. These and other variations are withinthe scope of the invention.

While the invention has been described above by reference to variousembodiments, it will be understood that different combinations, changesand modifications may be made without departing from the scope of theinvention which is to be defined only by the appended claims and theirequivalents. Thus, instead of using the specific optical elements in thespecific order as described, including the placement of a sample cell,or sample collection in the beam path, other optical elements, opticalsystems, or arrangements may be used without departing from the scope ofthe invention. For example, the pre-encoder optic 36A used in FIG. 1 toform a dispersed image, could be a focusing grating, a plane grating andfocusing mirror or lens, a grating pair, prism pair or prism-gratingcombination, a grating pair, prism pair or prism-grating combination anda focusing mirror or lens, a prism and focusing mirror or lens, and thepre-encoder optic 36A used in FIG. 1 to form an extended image caninclude a simple focusing mirror or lens, a camera lens system, aninterferometer, or a focusing mirror or lens and collection of bandpassfilters or a linear variable filter. In addition, various light pipes,waveguides and optical fibers (and collections thereof) can be used tobring the input radiation from or direct the encoded signal to a numberof remote sampling stations. When considering analyzer systems thatmeasure radiation emitted or scattered by a sample or collection ofsamples in response to excitation radiation, the position of the encoderbefore the sample or after the sample is somewhat arbitrary. In thefirst case, the excitation radiation is directly encoded, and theresponse radiation is (subsequently or indirectly) encoded. In thelatter case the response radiation is directly encoded. For asufficiently fast and linear excitation response, the response radiationis encoded exactly the same in either case.

Where the modulator 22 of FIG. 1A and the modulators of the variousother embodiments in the other figures are designed to be rotated aboutaxis 40 to encode corresponding radiation components, the filters on themodulators occupy annular regions of the disk as shown in the variousfigures of this application. This invention, however, is not limited tosuch implementation. Instead of annular regions, the filters, such asfilters 50 a, 50 d may form four linear rows on the surface of themodulator, and the modulator may be reciprocated linearly along adirection substantially parallel to the rows of filters, or rotated as adrum. The target image 52 is then projected in a direction with itslength transverse (preferably perpendicular) to the direction of therows of filters so that the image overlaps preferably all four rows ofthe filters. Such and other variations are within the scope of theinvention.

Where the radiation filters and filter pairs of analyzer 100 of FIG. 1Aare described having a continuum or three or more distinct levels ofcontrast, the various embodiments and examples described above can beembodied using binary modulation encoding, albeit with substantiallylower performance. Such and other variations are within the scope of theinvention.

The numerous embodiments of the invention should be considered as designstrategies that can be used in various combinations to facilitate agiven spectroscopy or imaging application. In particular, modulatorpatterns comprising various combinations of radiation filters and filterpairs shown in this document are within the scope of the invention.

1. An encoded filter-correlation radiometer for measuring a sample,comprising: at least one source providing broad-band radiation in atleast one spectral range; a two dimensional spatial radiation modulatoroptically coupled to the at least one source, rotated about a rotationaxis, and positioned in a plane so that an encoding axis of saidmodulator is substantially along a radial axis of said modulator, saidmodulator having at least three radiation encoding filters at differentradii from said rotation axis for modulating intensities of radiationfrom said source as said modulator is rotated about said rotation axis;optics for collecting and directing radiation to the modulator so thatsaid radiation forms at least three sub-images along a radial axis ofthe modulator, said sub-images modulated by said radiation encodingfilters to provide a modulated beam; a detector for providing an outputin response to the modulated beam; and a computer for analyzing signalsgenerated by said detector in response to said modulated beam to measurecharacteristics of the sample; wherein the at least one source isoptically coupled via an optical path from the at least one sourcethrough the optics and the modulator to the detector, wherein theoptical path also comprises the following in any order anywhere alongthe optical path except for between the optics and the modulator: atleast two target wavelength filters, each said target wavelength filterhaving substantial optical transmission attenuation in said spectralrange, said optical transmission attenuation a function of one or morespectral properties of a corresponding target analyte in a sample; atleast one reference wavelength filter, said reference filter havingsubstantially less optical transmission attenuation in said spectralrange as compared to said target wavelength filter; and a samplecomprising at least one target analyte.
 2. The radiometer of claim 1,wherein the at least two target wavelength filters and the at least onereference wavelength filter are located along the optical path betweenthe source and the optics.
 3. The radiometer of claim 1, wherein each ofsaid at least two target wavelength and reference filters comprisemulti-dielectric layer bandpass filters, etalons, dichroic mirrors,partially transparent or reflective solids or radiometry correlationcells containing a gas or liquid.
 4. The radiometer of claim 1, whereineach of said at least two target wavelength filters comprises a vesselcontaining a known concentration of a target analyte, said targetanalyte having substantial optical absorbance in said spectral range,and each said reference wavelength filter comprises a vessel containinga reference medium, said reference medium having substantially lessoptical absorbance in said spectral range as compared to said targetanalytes.
 5. The radiometer of claim 4, said target analyte comprising anominal constituent of natural gas.
 6. The radiometer of claim 1,wherein the optical path further comprises one or more additionalwavelength filters to reduce the intensities of spectral components insaid spectral range not useful for measurement of said correspondingtarget analyte, or to reduce the intensities of spectral features ofselected analytes different from said corresponding target analyte. 7.The radiometer of claim 6, wherein each of the wavelength filterscomprises one or more dichroic mirrors, bandpass filters, and/or cellsfilled with various gasses or liquids, including one or moreconstituents of natural gas.
 8. An encoded filter-correlation radiometerfor measuring a sample, comprising: at least one source providingbroad-band radiation in at least one spectral range; a two dimensionalspatial radiation modulator optically coupled to the at least onesource, rotated about a rotation axis, and positioned in a plane so thatan encoding axis of said modulator is substantially along a radial axisof said modulator, said modulator comprising a substrate and at leastone radiation filter pair, said radiation filter pair comprising tworadiation filters located at different radii from said rotation axis,each of said radiation filters modulating the intensity of radiationfrom said source, said radiation filters having substantiallycomplementary modulation functions, said radiation filters producing asingle encoded component of a modulated beam where a characteristic ofsaid encoded component is determined by the relative intensities ofradiation incident on said radiation filters, as said modulator isrotated about said rotation axis; optics collecting and directing saidradiation to the modulator so that said radiation forms at least onepair of sub-images along the radial axis of the modulator, each pair ofsub-images corresponding to a radiation filter pair of the modulator; adetector providing an output in response to the modulated beam; and acomputer analyzing signals generated by said detector in response tosaid modulated beam to measure characteristics of the sample; whereinthe at least one source is optically coupled via an optical path fromthe at least one source through the optics and the modulator to thedetector, wherein the optical path also comprises the following in anyorder anywhere along the optical path except for between the optics andthe modulator: at least one target and reference wavelength filter pair,said target wavelength filter having substantial optical transmissionattenuation in said spectral range, said optical transmissionattenuation a function of one or more spectral properties of acorresponding target analyte in a sample, said reference wavelengthfilter having substantially less optical transmission attenuation insaid spectral range as compared to said target wavelength filter; and asample comprising at least one target analyte.
 9. The radiometer ofclaim 8, wherein the at least one target and reference wavelength filterpair are located along the optical path between the source and theoptics.
 10. The radiometer of claim 8, wherein each of said target andreference wavelength filters in the at least one pair comprisesmulti-dielectric layer bandpass filters, etalons, dichroic mirrors,partially transparent or reflective solids or radiometry correlationcells containing a gas or liquid.
 11. The radiometer of claim 10,wherein said target wavelength filter in the at least one pair comprisesa vessel containing a known concentration of a target analyte, saidtarget analyte having substantial optical absorbance in said spectralrange, and said reference wavelength filter in the at least one paircomprises a vessel containing a reference medium, said reference mediumhaving substantially less optical absorbance in said spectral range ascompared to said target analytes.
 12. The analyzer of claim 11, saidtarget analyte comprising a nominal constituent of natural gas.
 13. Theanalyzer of claim 8, said characteristic of said encoded componentcomprising magnitude and phase of a signal.
 14. The radiometer of claim8, wherein the optical path further comprises one or more additionalwavelength filters to reduce the intensities of spectral components inat least one spectral range not useful for measurement of saidcorresponding target analyte, or to reduce the intensities of spectralfeatures of selected analytes different from said corresponding targetanalyte.
 15. The radiometer of claim 14, wherein each of the wavelengthfilters comprises one or more dichroic mirrors, bandpass filters, and/orcells filled with various gasses or liquids, including one or moreconstituents of natural gas.